It just dawned on me...I didn't realize it before probably cause I'm atheist but dont people tend to seek comfort in higherpowers/gods when they experience desperation and suffering?

So wouldn't edelgards war , which causes mass unrest, death, suffering, famine, etc. Actually cause more people to wish for salvation/intervention from a the Goddess?

No doubt about it, which is a huge part of what makes her zeal to destroy it so horrible. And what makes the CF endings where it does stay but only when directly under her supervision so insidious. She takes away the means in which people find comfort, only to "remake" it so that she has say in how the belief is practiced.

The Church was always its own entity, mostly leaving the surrounding countries alone - it'll intervene when asked to or when attacked, but otherwise they tend to stay out of everyone's business. When Byleth takes over, they either do so alongside the ruler of Fodlan (AM) or they are the only available person left to rule (SS/VW) since they are the one the people want to lead them. There's either a distinct separation between the Church and the ruling party, or there's no other choice but to have the two parties merge. Plus, Seteth and Flayn are there to help Byleth lead the Church in all cases of them leading it (with SS even allowing for the chance for Rhea herself to help).

That's, um, not quite the case with Edelgard. She actively kills/disposes of every other possible ruler with the explicit purpose of ruling over their lands and for Adrestia to be the only one there to control Fodlan. So her killing Rhea, Seteth, and Flayn (or forcing Seteth and Flayn to leave Fodlan) before going on to take control of the religion that was about their mother, well, could only ever really be for one reason; further control.

She already spies on the populace, as seen from Hubert's ending with Dorothea. She enforces a secret police as seen with Hubert's ending with Shamir. She indulges in censorship in her ending with Dorothea. And, again, she's purposefully killed off anyone that could stop her or challenge her control. Not exactly the longest stretch in the world that she also does what she does with the Church to get more control, considering everything else she does. Now the people who were so devastated about losing their religion totally no longer have to worry - now that it's been fixed and is being led by a good human, they are allowed to practice it with no fear of consequences! ...yeah that's gonna get a yikes from me lol.

And the thing is, even if I'm way off base and that's not meant to be taken like that... what you said is still very much true lol. Like, I'm far from religious, but somethin' tells me that for many religious folks extreme hardships would, like... just make them more ardent believers? And/Or that it would, uh, not exactly soothe them to see their religion mercilessly attacked and destroyed, only to be taken over by its destroyer? There'll be some who drink the Kool-Aid like Manuela, but I don't think the majority of believers would exactly be happy with Edelgard once her war is finished