yet it is SA that has constantly said it wants to destroy us
This is incorrect. SA has never said that. It is not now, nor has it ever been, the policy, expressed or implied, to desire the destruction of Asylon. Some in Astrum have that opinion. As the war progresses, that opinion spreads.
Do some people in SA want to see Asylon destroyed? Sure. Just like some people in Asylon would love to see SA destroyed. (Don't deny it, we already know it's true.) But taking the opinion of one character in SA and extrapolating that to the official policy of SA would be just as wrong as taking Glaumring's personal opinion and declaring that the official policy of Asylon.
and rule all of Dwilight under one faith and the prophet.
Guilty. Sorta.
SA isn't the standard, generic religion that "just wants to be friends". It has from the very beginning expressed a desire to spread its faith across the entire island.