It's possible the TSA was off the reservation in this case.

It's also entirely possible (and not uncommon) that the intelligence sources which led to this action in the first place are very sensitive and cannot be divulged in an open court. In that scenario the government has to decide whether to blow the source or to let someone off the hook to protect the source.

But I suspect the guy is innocent, if he was a bad guy he probably would have absconded overseas when he found out they were on to him. The fact that he stayed and forced the issue supports that.