In principle, nobody is ever stopped from entering the US for their political beliefs, he said.
Some reports in the Pakistani media have said that Khan, the chief of Pakistan Tehrik-e-Insaf party, was quizzed by the American officials as his US visa did not permit him to engage in fund-raising activities, which was apparently one of the main reasons of his visit to the US.
Khan was also questioned about his opposition to US drone strikes, the reports said.
Hoagland said countering terrorism is "most important" in US-Pakistan relations.
"The sooner we contain terrorists, the more peaceful the methods (of counter-terrorism) will become," he said.
The "strategic pause", an interregnum in the difficult relationship between the two countries, was now making way for a "more mature but restrained relationship" based on diplomatic, military and intelligence cooperation, he said.
Hoagland further said that no matter who won the US presidential polls, there would be "no pendulum swing in foreign policy."