That's what I would do, just keep an eye on it. IIRC popeye is caused either by bad water quality or an opportunistic infection that makes fluid build up in there. Did he come from a bad tank maybe?
If you are worried about bloat and the other fish are still eating it might be worth it to soak their food in the epsom salt solution in the hexamita thread. if they don't have anything it will just act as a laxative but if they do that should kill the parasites. Vacuum really well after.
Also sorry about you having to kill your fish, I hate having to do that but sometimes there's nothing else you can do.