Making a Hunter Question His Moral High Ground: How To?

Well, a lot of the draw of Hunter is moral ambiguity, and for an antagonist-or maybe a PC-I want to create, making hunters wonder who the real monster is is his goal in life.

Edit: I had a cool idea here, but I hadn't read enough of your post and it was ultimately irrelevant to your question. So to prevent any derailing potential, it has been removed.

In general I think it takes a person acting as a funhouse mirror to make someone question their moral high ground.  Emulate them, exaggerate them, twist them all out of proportion, but make sure to make it obvious that this could be them.

I find that just strictly enforcing the normal Morality rules while Hunters go about pursuing the Vigil is usually more than enough to make them seriously question their moral superiority, especially for players that have any hope of maintaining a 'normal' life for their character.  Remember, by the default rules even killing a Werewolf or Vampire is a sin, not just a challenge, and only the most alien monstrosities are immune to morality complications.

You won't be able to morally challenge people who refuse to be challenged.  I've seen players drop to Morality 2 simply because they were lucky enough to not accrue any derangements.  If the players, and the character, think they are right, then no amount of system nor story will convince them otherwise.

If you have those kinds of characters and players, it is best to drop the moral side of Hunter altogether and stick to survival horror--or maybe even paint them as doomed heroes.  You have to roll with what you have.

GARdian:

You won't be able to morally challenge people who refuse to be challenged.  I've seen players drop to Morality 2 simply because they were lucky enough to not accrue any derangements.  If the players, and the character, think they are right, then no amount of system nor story will convince them otherwise.

Derangements or no, a Morality 2 character is gonna be that creepy guy you want to avoid for no apparent reason. I'd start tacking on some negative modifiers to anything that isn't Intimidate in the Social Skills. I'd make contacts and allies not want much to do with the character. Basically anything that deals with people would suffer. Unless you are ditching Morality altogether, it's part of the STs job to make that low Morality uninticing, IMO.

Make an foil for the charaters.  Copy and then exaggerate them.  Also, for members of the Long Night or other faith-based cells, break them.  Introduce the fact that God is indifferent to is plights.  He just doesn't care. For Null Mysteriis, make them see that, no matter what they do, that there is no order in the universe and nothing that they do is meaningful.
For vampire, make a point that humans change the flesh they eat to make it seem less gross.
Or, better yet, put a charter between a rock and a hard place.  Make it so a Mage is the only one with the information that can stop the monster, but she won't give it to the cell because the cell killed her sister a week ago.  So the Mage, in addition to coming after the cell, is more then content to let the cell stew in the knowledge and guilt that, if they hadn't been so blinded, they could have stopped it.

GARdian:

You won't be able to morally challenge people who refuse to be challenged.

No, but you can challenge their characters plenty.  There are a handful of mechanics that can be used to influence the results of a Morality check (at the very least imposing flat penalties to the roll based on the callousness of a particular act) and Degeneration roll. To keep Morality higher on average, give bonuses to this roll.  To represent a character doing something particularly over the top, or what could be called subjectively 'bad' in your chronicle, impose a penalty to it instead.  To make going crazy because you act crazy more likely, impose penalties on Degeneration rolls, etc. If you think a character is already crazy enough to help describe their actions, give bonuses instead ("Well, it appears that your current insanity is buffering you against further degeneration, take +2 dice. Funny how that works.")

JNewman:

Derangements or no, a Morality 2 character is gonna be that creepy guy you want to avoid for no apparent reason. I'd start tacking on some negative modifiers to anything that isn't Intimidate in the Social Skills. I'd make contacts and allies not want much to do with the character. Basically anything that deals with people would suffer. Unless you are ditching Morality altogether, it's part of the STs job to make that low Morality uninticing, IMO.

A minor inconvenience, really, and one that is likely to drive a wedge between you and the player(s).  The player believes he is right, the character believes he is right.  They're only going to view this as unjust punishment for doing the right thing.

QualitySteel:

No, but you can challenge their characters plenty.  There are a handful of mechanics that can be used to influence the results of a Morality check (at the very least imposing flat penalties to the roll based on the callousness of a particular act) and Degeneration roll. To keep Morality higher on average, give bonuses to this roll.  To represent a character doing something particularly over the top, or what could be called subjectively 'bad' in your chronicle, impose a penalty to it instead.  To make going crazy because you act crazy more likely, impose penalties on Degeneration rolls, etc. If you think a character is already crazy enough to help describe their actions, give bonuses instead ("Well, it appears that your current insanity is buffering you against further degeneration, take +2 dice. Funny how that works.")

I reiterate my above statement.  If the player and the character think they're doing good, then you won't be able to change their mind at all.  At best, you'll simply force a change in behavior to avoid the mechanical ramifications, at worst the player will leave.

Do you want to challenge Hunter NSCs or Hunter SCs?
From your Post i would have thought NSCs, and to challenge their sense of 'rightness' a little more info about their victim might be all that needed:
The Family of a vampire he still tried to keep save no matter what and which is now gobbled up some misfortune or another.
The werewolf who worked charity for no sinister or selfish reason.
The Mage who always gave beggars his smallchange.
I do not think btw that this compact or conspiracy-connect. After all, all hunters are humans with human lives they try to preserve of salvage, with human parents and maybe children, with human friends, etc.
Basically if you show a hunter that his 'targets' are human, or more precise, like him or how he thinks he should be, that will blurr the compass.
As for your example of the Long Night: Did you ever, i mean EVER meet somebody how really believed and still gave a crap of the supposed origins of the bible? If you believe it is directly from god, even though you might take a bit of a dim view of the old testament when you are less of a fire&brimstone-type because leviticus does not really match up with the laws given by Jesus which are basically a raising of the 10 commandments to level were breaking them in your own mind is a sin you should atone for.
The long night, by the way, is most likely doing it for a much more simple reason:
The 'witch' is different and he is not sure if she is a danger and so he decides to take the safe road. Everything after this is just compact-specific rationalization of guilt. The reason whoever does not change and that is way i think it is the best way to target the underlying reason instead of its symptoms.
As for 'breaking their faith':
There is no reason why that should quench their thirst for vengeance or destruction. They do not kill because they believe. They are willing to believe because they are willing to kill. And they will not use this because they loose their faith.
In some cases they might not know how to rationalize and go either Slayer or stop till they found a m.o. that allows them to go on. But the moment of 'Oh my god, what have i done' comes not when you convince them that god does not exist or care but when you realize that you might have been wrong.
And that could be for any number of reason, though the most likely is seeing the humanity in 'the enemy'.

GARdian:

A minor inconvenience, really, and one that is likely to drive a wedge between you and the player(s).  The player believes he is right, the character believes he is right.  They're only going to view this as unjust punishment for doing the right thing.

That's a fish of a whole different flavor, but I still stand by my post. If you want them to understand consequences for their characters, then there need to be some. If a player gets mad because their character is suffering consequences, well, either you can try to explain what is happening and why, you can ditch morality altogether (which sounds like what your group wants, tbh), or you can find a different group to play with. I have no patience for the no consequences crowd myself, but to each their own.

This is not about consequences. The way i figure it consequences are totally independent from whether or not you have the moral high ground.
This is about Morale and the Morality system is only able to picture a very small part of that.
Consider the following:
The Hunters just killed something or someone. A real menace and danger to society.
And the next day they find out that this person was kind to his mother and was a good father.
Or something along that line.
By this point they will already have made their Morality-Checks, most likely with a bonus and are out of it, one way or another.
But the recognition of the 'human' background of their enemy might make them doubt their high ground nevertheless.

With players who are simply not sensitive enough for shades of grey and nuances this is, of course and obviously, a futile attempt.

GARdian:

If the player and the character think they're doing good, then you won't be able to change their mind at all.

You might not be able to.  I have more faith in my ability as an ST than that, however.

QualitySteel:

You might not be able to.  I have more faith in my ability as an ST than that, however.

I think you're missing the point.  It's like trying to shout at the deaf.  No matter how loud you are, they still won't be able to hear you.

If a player has made up his mind about being right, then that's the end of it.  He'll never see it as murder or torture.

GARdian:

If a player has made up his mind about being right, then that's the end of it.  He'll never see it as murder or torture.

When his character becomes a slasher NPC, then he'll listen.

I may like D&D, but this isn't it-if a player wants to be like that, he shouldn't be playing a game specifically devoted to RP challenges.