I think the problem I had with it had to do with the way the sentences were constructed. For example:

"... this could have been a disaster, very much like the rubygems.org security breach in early 2013"

This implies that the issue you had wasn't as serious as the RubyGems issue.

Similarly, the following sentence likewise implies that the breach was not as severe:

"Unlike that incident, there’s no evidence that, other than ourselves, the engineers who reported the bugs, and a few members of the GitHub security team who knew about the issue, anyone knew about this hole."

This implies a confidence in the presumption that you weren't breached that you then backpedal on in the following sentence by saying "of course we're not positive because we didn't have logs".

Both of the sentences I cite lead a reasonable reader to a different impression than the one you say you were attempting to convey. I'm glad to see you clarify things here, but I hope you can see why people would misconstrue things based on the words in the post.