Spoilers on several routes below
It is DEFINITELY not my impression that the writers think the Church is good and Edelgard is bad. Rhea is the classic Evil Pope for all of act 1 and even goes crazy (and turns the whole church crazy along with her) in the Church route, which makes no sense if the writers are trying to present her as the wronged party here. Rhea and Edelgard are both extremely gray characters. With the issue of Edelgard’s route being short and unsatisfying re: Those who Slither, I imagine it’s a mix of things: it is traditional for an FE the final fight to be against The Dragon (and from Edelgard’s perspective, it’s foolish to antagonize Those Who Slither before defeating Rhea, as she would be fighting on both fronts), and also possibly straight running out of time. There are a lot of reused maps, cutscenes, etc., that speak to a lack of time, and the BE route is already actually two routes. Also, each route is (probably intentionally) incomplete in terms of the Big Picture, and since the Church and GD routes focus on Those Who Slither, they probably just cut it from BE for scope.
I think it’s a shame, because Edelgard’s route definitely could have been tinkered with to provide better closure than a “she killed the bad guys later!” ending narration, but I really doubt that it’s because of the game’s preference for Rhea over Edelgard. If anything, the game seems to heavily champion Edelgard compared to what she objectively does (start a bloody conquest war) by giving her somewhat unrealistically noble motives/ending. (Like, most revolutionary dictators don’t overthrow the corrupt system via bloody war and then say My Work Is Done and peace out, you know?).