Rudeus doesn't see those two in that way at all, so it wouldn't have happened on its own if he had stayed either. So no, the 'regret' cannot be that.
He's loyal to Sylphiette and thought Paul was trash for cheating on Zenith. He's consistently refused any hints toward that effect from the two beastgirls. Really wasn't an option that Rudeus would ever consider outside of Hitogami bringing it up, quite obviously so as he immediately refused in the dreamspace.
It's super suspicious that Hitogami wants Rudeus rooted here in the Academy city and not out adventuring.