Suggestion:
Only use SVN manually if you have no other option left.
I agree with the solution proposed by Chris. This way you also ensure that other people downloading the project will get the correct name. (I would have written a comment on his answer but comments are limited in length)
By the way, the project directory name itself is not versioned. The Modeler does not care what it is called. By default it is called "MyProject-main" but it can be called anything. You can rename it and then reopen the .mpr with the "from disk" option and everything including version control will work. But this fixes the name only locally.