Strategypage has a good summary of the players in Pakistan. I'd fail to do it justice if I summarized it. Just go read it.
Here, some urge us to dump Musharraf with the view that his opponents are democratic saints.
Others urge us to back Musharraf to the hilt and help him maintain his dictatorship against corrupt politicians trying to engineer a return to power.
The existence of Pakistani nukes makes the issue far more important to us than it otherwise would be (And isn't this alone an argument to fight nuclear proliferation? Do we really want to be drawn into every Third World political crisis?).
The truth is that Musharraf is a decent ruler who rules by means that cannot maintain public support for long. I've long wanted us to push Pakistan to democracy and end military rule to prevent jihadis from exploiting the public's outrage over the lack of democracy.
I hope that Musharraf manages to bridge the divide between military rule and the corruption that has plagued Pakistani democracy. If Musharraf can shed his uniform and win an election against the representatives of the old regime, he might be able to rule honestly enough within a democratic system to keep the military out of politics and break the cycle of deadening corruption followed by military coup that only seems to benefit jihadis who oppose both corrupt politicians and mlitary rule.
It's a gamble however we play this. You do know this decade sucks, right?