Nah, that's what he did: Slept with Thomas while he was with Will. That's how Thomas knows what happened between them, and let's the scene work as written still
Sure, that's the reality of the scene in question. But for the sake of the silly meme, I'd like to think that O'Brien violated some cardinal/unspoken rule for hooking up.
Man why does everyone blame O'Brien for any problem with transporters? He never even served on the Potemkin! I'm sure if he was Chief, he would have made sure to disintegrate Tom right then and there