Please ignore my previous message and patch. Although it installs a pip script into the virtual environment, the script's shebang points to the global python and not the venv python. I'm trying to figure out why this is, but the pip voodoo is way deeper than I understand. I can only guess that it has to do with sys.executable which appears to point to the normalized path, i.e. the system python instead of the symlink inside the venv.

So I tried dstufft's other suggestion: disable system site packages before bootstrapping pip and then re-enable it afterward. This actually does work in an end-to-end test on my system. So I'm attaching another patch that applies to python 3.5 (1b279c2 on github -- I don't know the equivalent mercurial hash) that is smaller than the previous patch. I don't know what the side effects are of monkeying around with system site packages like this, so apologies in advance if this is a stupid thing to do...