Clearly he was wrong, but it's easy enough to believe the pseudo-military of the future operates on differing principles to the armies of today.
He couldn't be "wrong," because Starfleet doesn't exist. He was being inconsistent, which is quite another thing - but he was making this stuff up, he was the final authority on it while he was alive, and if he chose to be inconsistent that was his call. People can disagree about the importance of consistency and about how much to privilege the contradictions in Trek that they like over the contradictions that they dislike, but calling Roddenberry "wrong" is trivial and meaningless.
I didn't say GR was wrong because he "violated canon" or anything like that, but because that particular decree didn't make much sense. The ship was armed to the teeth, for starters.
And whenever there's a war on in Star Trek, it's Starfleet that fights it.