The "government" didn't own it, Charlie Wilson did then the University. In any event, the government, through ATF, approved the transfer to the University via a Form 10. So it was legally owned by the University Museum. When the receiver was destroyed, the "gun" ceased to exist as far as ATF is concerned, all that's left was a pile of parts that are not a gun. Assuming the destruction was done properly, ATF is out of it.
Now, who authorized the destruction and sale, who got the money, etc. is the question that might yield charges. Most likely just a local PD, unless the sale over state lines brings in the FBI.