I haven't played the other routes, but I'm playing the BE route and I don't see what's so wrong with what she doing. The church needed to go it as corrupt.
Yeah...... but the reasons for that - which the BE route either glosses over, changes exclusively for their perspective but none of the others, or outright misrepresents - is probably the biggest issue most have with the game's story altogether. Like there are certain motivations and opinions and effects that all guide characters in different directions. That's cool. The problem is what actually happened leading into the events to start the game and why. And the BE route simply doesn't add up.
Even Edelgard's relationship with the people in BE house along with the prof makes no sense. Mainly because Edelgard starts off knowing a substantial deal more than the vast majority of the characters in the game and makes decisions
counter to what her own interests are to fulfill some trite new world order shyt. The game dumbs itself down just in the BE route by giving Edelgard some weird determination mantra to round the edges off - and people generally understand why after getting the full picture.
The developers/production simply didn't want to commit to portraying one of the most identifiable characters for the title as a self serving Nazi more or less
coherent plot be damned.