Johnny Fontane staying in the room.

I'm referring to the meeting with Moe Green.

In the novel, most of the people in the room leave (even Al once Michael gives his OK).

I get why Tom, Fredo are still there, but why Johnny, he's not in the business...

You're asking why, in the movie, Johnny stays in the room? My guess is that it would just break the emotional momentum of the scene, for everyone to say goodbyes to him.

I think the explanation is pretty simple: the band and girls were not to be privy to family business and Michael needed to talk to Johnny as he, indeed, did.