Okay, let me paraphrase some things.
1. Edelgard wasn't destroying the entirety of religion. She's just destroying the corrupt clerics in power.
2. The whole "Petra is essentially a prisoner" thing is wrong. I mean she automatically joins you in Crimson Flower, and Edelgard gives her autonomy at the end. She even does this in the other routes that aren't Crimson Flower.
3. I'm not wholly on "the ends justify the means" either. Like, I will heavily criticize an experiment if it does something horrible. But you really have to consider that a war was basically inevitable. TWSITD was still rampant, and TWSITD had nukes to destroy all of Fodlan in their possession. It is canon that Edelgard kills TWSITD after the route.
4. Edelgard does acknowledge she did stuff wrong. She is surprised when Byleth joins their side.
5. I mean Edelgard does kill TWSITD, and in the other routes, they still live. The problem is that Edelgard had to find a way to defeat TWSITD without them nuking the entire continent. They had so much power over the continent. It was very rough, but it was the only way that they could defeat TWSITD and destroy the system alongside with it. And she managed it. Just because Thales dies in the other routes, doesn't mean the group itself is over. They probably had to go through a long and tough war to remove them too.
6. How else was Edelgard supposed to stop TWSITD and Rhea? Was she supposed to be nice to Rhea, the upholder of the system she disagreed with? I mean even Claude wasn't fond of Rhea. He respected Edelgard, despite being enemies.
I'm not one of those "Edelgard did nothing wrong" people, for sure. I acknowledge she did wrong things. But she did some great things too. Honestly, almost every major character in Three Houses has done something wrong.
Yes, people do suffer in war. But read my points. And it is not like their lives were so much better in the noble system either.