Fix over-aggressive sys.modules scrubbing for namespace packages.

Testing Done:

This bug manifested itself when running our internal pants in a virtualenv
that already had pants installed, resulting in some bizarre conflicts of
namespace packages.  I verified the fix by manually patching this version of
pex into the existing pants internal pex.  However I could not come up with
a succint unit _or_ integration test to cover it.

Existing tests continue to pass: https://travis-ci.org/wickman/pex/builds/41673725

Reviewed at https://rbcommons.com/s/twitter/r/1378/