Could the same thing be said for JFK?
Not really. Had there been any active, credible threats against JFK the Secret Service would have forced him to ride in an enclosed limo, as opposed to allowing him to ride in a convertible.

And whilst Al Quaeda may not be to blame for this one, sure as eggs are eggs they're going to find it a lot easier to operate in a panic-stricken, angry, unrestful nation.
In all actuality, this makes no difference for AQ, as the area they operate in is under the control of no one. If you look at the borders in that area of the world on most maps, they are dotted lines. The border areas are under the control of mountain tribes who haven't been under anyone's control for centuries. Besides, angry and unrestful (restless?) describes Pakistan's entire history, not just the past few years. Panic stricken? Probably not in the least. Assassination is business as usual for Pakistan. Again, just look at their history.