I won't dispute that there are writing issues, but Edelgard's arc isn't a redemption arc. She does display some remorse, but that's not who she is.
The "feels bad" vibes come from support convos and just the whole game really (special mention to the final Dimitri moments, pure tragedy).
That's the whole point, she's well meaning but arguably isn't a "good person". You're not playing (well, following) the usual hero in disguise, the good hearted gruffy hero. She's an actual anti-hero. She does real bad things in order to achieve her goals. And while she's conscious of what she did, she did it anyway. And would do it again if the circumstances were the same (she does wish the circumstances were different, but alas, that's not the case).
Most game plots are written so that the player always have the moral high-ground, even if they may commit questionable acts. That's not the case here. She's the aggressor. She's the one who wants to burn the old shitty system to try to replace it with a less shitty one. While she does technically react to the world of Fodlan (*), she does not react in storytelling terms. She acts. So by siding with her, you're not playing the "restore order hero" (which is way too common for my taste), you're playing the "revolutionary hero", with all that entails in terms of aggression.
(*) She wouldn't wage war if the Dubsteppers didn't experiment on her and/or if the church wasn't so oppressive and/or if the crests weren't the source of so much suffering.