Truthers are silly. But any person that thinks there aren't details about 911 that remain heavily classified is just as clueless. In the case of Pete, he had a chance to meet with a high ranking member of the armed forces and used that chance to ask questions. It kind of reminded me of how one of the first things Bill Clinton did after becoming president was to inquire about extra terrestrials, AREA 51, etc. Hell, I'd do the same thing.
Unfortunately, the military source did not take kindly to the questions and it ended up a miscalculation on Pete's part. It doesn't mean he's a truther, it just means he has a curious mind. Curiousity is one of the stronger indicators of high intelligence. I don't see any reason to hold that against him.