That was not on her, he wasn't raised to be king and the crown was too heavy for him to handle. She single handedly took back control from that religious cult and all the people that were trying to manipulate the king. Tommon and Joffrey's failures were because their father was a drunk abusive asshole.
Yes it was, Tommen loved Margeary, and he also knew Cersei prevented him from going to the Baelor Sept that day it blew up, so he knew she did it. Also, Robert wasn't his father, Jaime is and he knew that.