They literally have the source of all the Farley church's blessings on their island, who happens to be a dude who would HATE the church once they told him what's happened. They have such a massive upper hand in any negotiation with the church that it's laughable.
One question: Why are they in a weak position?
The church's trump card against the witch is Rukia because of her three blessings.
But the MC and his friends have the "Patriot Saint" a.k.a. the creator of those "gods" in their hands.
They could just threaten the church to kill him and therefore "erase" the "fods" and all "blessings" - including Rukia's.
So they can actually "erase" the church's trump card against the witch.
Furthermore the people on the island are people who were mostly banished there for having the mark of an unknown "god".
All "gods" created by the "Patriot Saint" are known, so those unknown are not created by him.
That means even if he dies, the people banished to the island would NOT lose their powers (except for Rosa).
So unlike the church they have nothing to fear from the "Patrot Saint's" death.
Of course, the MC does not intend to kill the "Patriot Saint" but that is something the church would not know.
And given the circumstances above they would very likely believe that the people on the island would really kill the "Patriot Saint" as it is only beneficial to them.
They're in a weak position because they don't have enough cards to play. They have 4 people with Blessings, Abyss, The Great Hellfire Mage Cutie, Warriors-kun, and 3 mages. The Church knows about 0 of this. You can't threaten them without revealing your forces. And if you do that, they can plot against you.
So, what happens if he reveals himself to be alive, and opposing them? They bring his Foster Dad and ask him to Surrender or he dies. None of the forces he can bear are a match for a Nation State. You can't fight an army with your small ragtag rebel group.
Farley isn't a real card to be put into play. Why? Because they woke him up. The Church assumes Rosa is Dead. And if they sacrifice Rukia to Kill the Witch, they no longer have a Blessed One with the Time Power. Which means Farley is going to age naturally and die normally. Which means, assuming the 13 Gods are linked to Farley, they also expect the pantheon to Die. So his death, doesn't matter to them. I agree with other commenters, that the Witch is most likely his Daughter, so they woke him up, to mollify the daughter, so the "Divine Retribution" can kill them all. But, if Rukia was the only thing that mattered to kill the Witch, they wouldn't have bothered to wake him up.
And all that, depends on the Church actually knowing or telling people things. They've destroyed all the knowledge of Alamira and the other "dark gods". After 1000 years, a ton of knowledge could have been lost naturally. Do they know Farley's life is linked to his Pantheon, they might not know that. So that's another problem with attempting to use his life as a bargaining chip.
And we have to remember. The Church has already won, this is the future they created. They destroyed Science and the Magic Stabilization Devices. So there is an automatic more powerful class of people. Aside from the Blessed Ones, they are secretly helping the Slave Dealers and others with less than savory reputations to traffic and control Mages. And female Mages always have Magic Children. The Church probably have a hidden army of Mage Soldiers that they've been breeding/indoctrinating.
