I'm gonna say, that as CinC, the pres knows a good bit more, and is privvy to more information that you or I could conceive, via FBI, CIA, NSA, State Dept (of course half of those 'don't exist' )

As far as Pakistan, you have to understand the way we do things. Everything is not always black and white. We play in the grey mud a lot. If something is strategically more important, we will white wash it and use it to our advantage. IE: Pakistan. It was stategially more important to use them as an allie, even if we had to muscle them a bit, in order to gain important grounds, air strips, intel, etc.

We actually go over stuff like this in some of my military classes