Issue spam (in the literal sense) definitely needs addressed as well: https://pbs.twimg.com/media/CYI31g1UQAUXQbs.png
It's my project, why can't I just delete issues like any other bug tracker?
So the issue isn't that GitHub didn't let them clean up the issues after the fact, but that there were no a) rate limiting options, b) user reputation options, or c) issue submission filtering options.
Any one of those three would have reduced the impact significantly.