[Vicious Love]

Not to diverge too sharply from the topic at hand(Something about elephants and waterplanes?), but it seems the Ark does NOT affect friendlu unholy troops. I happen to concur with this, thematically, but a good case can easily be made for the alternative.
Either way, thought that was something people might want to know, game mechanic-wise.

And it doesn't get much apter, than the Jesus analogy. Awww, yeah. Holy water purifies; it washes your sins/the devil out of you(Let's assume the two are interchangeable. Free will and original sin are no less self- and other- contradictory than anything else in the Good Book). If you['re more devil than man(Or woman, but the bible tends to kinda gloss over those), the process kills you.
As any good Christian'll tell you, the devil is any and all thoughts save "praise God". Ergo, all non-sacred troops have a bit o' ol' Scratch in them. The principle of Universal Christian Guilt dictates all sacred troops also possess some measure of sin, and are therefore just as damned to Hell as non-sacreds, but we shall assume, for the purpose of this thought experiment, that it is too miniscule a quantity of evil to visibly react to holy water, and requires a more rigorous form of testing, such as snake-handling or an inquisitorial pyre.
Wherein lies the crux(Our Father, pardon the pun) of the analogy: Degree of sanctity. After all, only truly wicked babies die in their sleep after merely being baptized, and only the possessed actually respond with epileptic seizures. Furthermore, only demons, vampires, and Muslims actually BURN, when exposed to the stuff. The aforementioned pyre, on the other hand, will burn the sin right out of anyone and anything. The process is the same, but intensities vary. Such is the Ark.

While I'm willing to grant that your pretender is more evangelist than saint, that hardly counts for anything in light of the fact that he wrote the Book. Honestly, a simple escape clause for divine atheists is all it would take.