Bob Owens at Confederate Yankee has the official word from Col. Steven Boylan, the Public Affairs Officer for Gen. David Petraeus:
To your question: Were there any truth to what was being said by Thomas?
Answer: An investigation of the allegations were conducted by the command and found to be false. In fact, members of Thomas’ platoon and company were all interviewed and no one could substantiate his claims.
As to what will happen to him?
Answer: As there is no evidence of criminal conduct, he is subject to Administrative punishment as determined by his chain of command. Under the various rules and regulations, administrative actions are not releasable to the public by the military on what does or does not happen.