Earlier quoted context omitted.
What are the set of commits that GitHub should allow people to make to repos that they solely own?
The set of commits that aren't directly trying to trick someone into installing malicious software. It's fine to host code that contains any instructions, as long as the intent of that code is not to trick someone into running malicious software.
In this case, if the author had updated the documentation sufficiently along with the change to make it clear what the new behavior was, that would have been fine?
I agree that malware is unhostable. And in this case I think the author crossed the line. But I am concerned about getting that line defined in a way that restricts project owners from making whatever changes they want in their own self-interest without tricking people, per se.