This email actually increases rather than decreases my trust in GitHub - it explains exactly what happened and answers all of the questions I might have about the incident. It reassures me that they take this kind of thing extremely seriously.
Yeah. Mistakes are going to happen and what really separates the good companies from the bad ones is how they deal with those mistakes. This seems to be a good example (for the reasons you stated). I have seen plenty of incident reports from other services that don't really tell me what happened or what exactly was done about it. That's when I feel unhappy. Within reason. I'd still be pretty unhappy if a company was really negligent, even if they had a really great incident report :P