Well taking into account that the Admiral was just going back to create an alternate and parallel time-line which would have no effect on the present as they understood it and stood upon, well that'd just mean that the Rhode Island wasn't on an urgent mission to save the universe... It was busy work. To stop pollution being ejected on their neighbours.
And Harry knew it.
Otherwise he was committing suicide when he let her go.
So really he must have been pissed off about being underutilized which is why he let her go despite orders, because her daft flight of fancy was really mostly harmless. Although, he wouldn't break orders if this was the forst time they'd given him a shit detail. obviously there would have to have been a clear pattern of the Admiralty having zero respect for the lad before he would flush his career down the toilet like that.