Tommen is a little kid with no authority. Everything of importance was handled by the Queen Regent. Also, Tommen (presumably) isn't a sociopathic monster like Joffrey was. Besides, if the Crown had any real authority over the religious nuts, she could just order herself released. And as Brando has said, we've already seen what Cersei is capable of. She's capable of completely ruining all the hard work Tyrion, Tywin, and countless others put in to try and ensure stability in King's Landing. She's a moron, an amateur at best who let her empty victory over Ned Stark go to her head and make her think she was some sort of political mastermind.
*edit*
Also, wasn't part of the reason Cersei agreed to let the army of the faith reform the fact that there was a severe troop shortage in King's Landing? Even if Tommen had the will and authority to order his mother released (in the books Margaery was released to the custody of someone else until her trial) he may not have the troops to enforce that order.