In this case I think the correct decision was made.
I can't speak for the general situation, but in this specific case I have to say I think the owner of the original Bebop package (Kelling) was at fault, for not ensuring that the correct email address was on file for his package. I don't think it's asking too much, if you're publishing a package to a public resource, for the onus to be on you to keep the correct email address.
Yes, I feel bad for him that he lost control of the package name, but some of the blame does lie with him. In the circumstances I think Github and the new Bebop owner handled it well.