As for the army captain or whatever her rank was, I could totally see her comment coming, and it made me cringe. I was expecting her to say it differently, though, more like, "He's very handsome," or "He's totally good-looking." Using the word "hot" made her sound like a teenager.
Actually, from this scene I got the impression that the Army had been chasing Superman around for some time (I'm thinking weeks to months) to "find out where he hangs his cape". And I'm also thinking that by now, it's kind of turning into a game between General Swanwick (and his aides) and Superman. When Superman tells Swanwick that the latter should intercede for Superman in Washington, Swanwick responds with a sort of good-natured exasperation. I think the Army captain is picking up on the lighter atmosphere and that's why she makes that unguarded comment.