He probably came up with that explanation to give to the press. Just because he had an explanation doesn't mean that his intent was based on following the flag code.
Again, the flag wasn't lowered when a dozen or so lily white rich kids in Newtown were killed by a non-Muslim, so I don't think you have a case to stand on there.
He's right, though. People are killed everyday in every way imaginable. I don't get the flag code fetish, nor do I expect an Alabama Republican politician to be perfectly fine with homosexuality, but is it really hard to believe that his personal beliefs-whatever they may be-have nothing to do with this?