I let him back in his cage with the rest of his flock but the leader kept picking on him. She did this last time I tried putting him back in but she isn't doing it as aggressively now. Before I had to take him out because she wouldn't leave him alone for 15 minutes straight but this time it only lasted 5 minutes, she wasn't as physical as last time either. They stopped now and all of them are eating the seeds I put out. (He was flying from dish to dish trying to eat, although I gave him his food earlier this morning). They seem to be calmed down at the moment.
*UPDATE* Shortly after I posted this the leader confronted him again and started biting his leg (there wasn't any visible injury to it), so I took him out and put him back in his separate cage. Maybe I'll try again tomorrow, depends on how well/active he is