Yes, fixing pip in this case is the right approach.

Since you're going to be including a copy of pip with your application, you can also just patch that yourself to get going while the pip team decides how to go from here. Or you could add a sitecustomize.py file (which will only be imported if you have "import site" in your ._pth file) that sets site.USER_SITE to something so that pip does not crash.