Who's the intended audience for your Github fork? Is there any likelihood of marketplace confusion?
If you're just forking a repo on Github and upstreaming patches, then the likelihood of confusion is minute. Github's users know what a fork means, and if they're the only audience, there's no problem.
If you break the upstreaming link, distribute release packages, market to non-Github-users, and so on, then the likelihood of confusion grows. At some point, a court would probably assess that trademark violation had occurred.
If you're just forking a repo on Github and upstreaming patches, then the likelihood of confusion is minute. Github's users know what a fork means, and if they're the only audience, there's no problem.
If you break the upstreaming link, distribute release packages, market to non-Github-users, and so on, then the likelihood of confusion grows. At some point, a court would probably assess that trademark violation had occurred.