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.