Yes he did. And how he obtained permission to travel there at a time the State dept considered Pakistan totally off limits is another story.
The same way people travel to Cuba now - they buy a ticket and get on a plane. Pakistan had no restrictions on travel by Americans, just as Cuba does not now.
If the State Department feels like it, they can exact a fine when the traveller re-enters America. I checked the numbers on that for a sister a couple of years ago - State mostly doesn't bother. I think it was about $100. I think the fact of the Pakistan trip is a non-story. The reason for the Pakistan trip might be interesting.