Look guys, the story's villains are doing villainous things! Who would have thought.
What's really the purpose of following along from the supposed "evil" side's perspective if you're going to make their antagonists this over the top crazy?
If you're going to do a switcheroo and have the MC be part of the generally perceived "evil" side, maybe paint both them and the antagonists in a grey spectrum rather than simply going with the standard of "MC gud, bad guys bad", which sort of ruins anything original the basic premise could have brought to the table.