While she's not often shown doing evil things, she is one of four incumbent generals of the Rokuhara regime. And while she does try her best to stop the other generals from carrying out their duties, it's usually for the self serving purpose of prolonging the suffering of Yamatoan citizens to bait the GHQ into war.
That being said, I love Ashikaga Chachamaru with every fiber of my being! If standing by her side condemns me to an eternity of hellfire, then I will gladly burn to have spent my life with her.