I think the reasonable response would be to take the website down and make the repo private while they change the name.

Yeah it's pretty clear that he's well-intentioned. There are plenty of ports of open source projects literally named "port of <trademarked name>" and generally the original authors don't mind. what even is the point of open source if you can't do that?

If I fork a repo on GitHub and the name of the project is trademarked, have I committed trademark violation?

In this case he just went a little too far by cloning the whole website. Even then tbh I still take his side because it's in the spirit of the Wild West Internet culture to have done something like this.