Yeah, Varys needs Cersei in control because she is absolutely terrible at it and it destabilizes the country. Unless there's a rather big change, I don't see Tommen doing anything against her in the show, and Varys will probably help her stay in charge just enough to piss off everyone in the 7 kingdoms and weaken as many of the houses as possible.Well in the books, before Varys kills him Kevan Lannister (the new regent and Lancel's father) visits Cersei in her cell and basically tells her she's through in King's Landing even if she weasels her way out of the charges.