I'm not quite sure what the feature is called — I can't find any references to it, which is part of the problem — but GitHub Issues allow response by email, which is then added as a comment on the Issue. I'd like to disable that because it adds too much noise to comments.
This is currently impossible to disable. There is currently a dear-github post about it, but GitHub has yet to respond. There is no mention of an ability to disable this "feature" in the release notes nor anywhere else that I could find.
I'd recommend putting something in your README about not using email replies, messaging any users who are particularly bad about replying to the emails, and editing issues to fix any problems when it does happen.