He wasn't the President then, assuming he is now. He was just a first term Senator.
I was at Camp Lejeune from '95 to '96. Clinton came just before Christmas (I can't remember which year) for a photo op. His advance people wanted to put up a background sign. I can't remember the verbiage, but it was just a little to political in nature. The CG said nope. The banner came down and was replaced by a big American flag. That's how it works. The President is Commander-in-Chief, but he's not the sovereign king. He has to follow the rules too.
If this Baghdad event happened the way it was described, which I believe is dubious, eventually there will be an investigation and the truth will come out - it always does.