He's not really fine though John chooses to ignore that as Rodney gradually gets back to work. Rodney's talking more now, almost back up to Rodney-speed as if he'd never been away, he's working and eating and the only time he seems different is when someone walks past and pats him on the back or shakes him by the hand. Then that deer in the headlights look is back and John can literally smell the fight or flight response on him. The only people he doesn't flinch away from are John and Ronon. John's a little jealous about that though he knows it's understandable. Ronon had been in the slave camp with Rodney and he seems to have become Rodney's protector both there and back on Atlantis. John can almost see the hackles rise on Ronon's neck when Rodney reacts at being touched by others. He sometimes thinks Ronon only allows John to get that close to Rodney because Rodney tacitly permits it.
There's no real closeness in their quarters though. Whatever intimacy they'd once shared is replaced by them simply sharing a bed though Rodney snuggles against him at night. The one time John had made overtures at more than that had caused Rodney to literally leap from the bed and cower in the corner, shaking. John hasn't tried since. He'd spent the entire night convincing Rodney to go back to bed with him and has no wish to repeat the experiment.
Rodney won't talk about exactly what happened in the camp and all Ronon has said is that it was brutal. John sees Rodney's eyes flick over to Ronon at the briefing about it and notes the grateful look in his eyes when Ronon doesn't elaborate any further. John wants to ask Carson about the exact nature of Rodney's injuries but he's not sure if he really wants to know until the night Rodney freaks out in his sleep and John decides the only way he can help him is to know the whole story. So he sees Rodney safely off to his lab and then goes to beard Carson in the infirmary.