The issues were deleted in fairly short order, but their notifications were still sent out to all repository watchers and persisted beyond the issue deletion. Also, most issues were generated mere seconds apart from accounts less than a day old.
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.
