There are rules about 'fraternising' in the military, although they're less strict that they were. IIRC, it's generally done that couples don't get to serve on the same ship or in the same deployment. I think the RAF maybe a bit more flexible about married couples. It's still frowned upon for someone to start a relationship with someone who is of significantly lower rank than they are, you often end up with accusation of favouritism from the higher rank to the lower and there's the question of the misuse of authority, similar to the way academic staff in Universities aren't supposed to be in relationships with their students.
I'm not sure how she could be stitched up, at least not in the sense I'd use the phrase. if you're not supposed to sleep with your crew,
don't sleep with your crew. It's not something you can do by accident, is it? There may be people taking advantage of the situation yes but (and there's nothing good about this, but it's true) if you're an officer you do need to play the political game, or at least be aware enough not to hand people who don't like you a loaded gun.