IMO, it was a smart thing to do. Rudy had a better handle on Arafat's character than Baker, Bush I, or Clinton, and likely has a better handle on Abbas than GWB. As do Gingrich, Hunter and McCain.
The various articles were at odds about that as well. most said he left "within 20 minutes", a few said he left quietly, a couple said he specifically stayed until "he wanted to leave", at least one said for 2 "somethings" (I'm sorry, I've forgotten what the name is for parts of music).
Rudy said so long as Arafat left before the "ode to joy" part, he missed the purpose of the symphony. That suggests that Arafat did not leave immediately.
But leaving quietly does not indicate acknowledgement of misconduct. Arafat had already gotten the political coup, having shown up, having been greated with admiration by others (one article said people lined up to get his autograph), and having sat through a portion of the music.
He could well have decided that, with Rudy ordering him out, leaving would be the best political ploy. It didn't turn out that way, so far as I can tell, over time more people supported Rudy than otherwise.
Again, I appreciate your questioning my position, as it led me to do more research and learn more about the event.