One theory as to why Rove isn't out the door

It is not just that he's Bushes "brain"; nor that he is owed a debt for building up Bush into the Presidency.

It is because Bush knew full well what Rove was doing the whole time. Rove gets indicted he'll have to leave, but until then, to dump Rove means the latter won't be the good soldier and spill the beans on how Karl and Georgie worked together to play some dirty tricks on a CIA Operative, which would mean the end of George Bush's Presidency and the GOP for a generation or two, for all intensive purposes.

Bush has always been a dirtier fighter than his father, just as there is no reason to believe he wasn't aware of Rove's earlier dirty tricks, there is no reason to think otherwise now, he has, at this time plausible deniability, but if he shits on Rove, he knows Rove will make him "fair game".