Kevin Flynn is a creator and his identity disc contains the ability to leave the grid and enter the real world.
Before his son was paged and entered the grid, why didn't Flynn copy whatever data he wanted to another disc (including the data allowing him to leave and enter the real world), delete those same parts from the original, and leave with Quorra to enter the real world, and destroy Clu from the outside?
I haven't seen the first Tron, the animated series or read the novelization, but given Flynn is a creator, disc copying doesn't seem impossible for him.
He could have left his disc for Clu to find just to bother him even more before removing him from the outside.