Make ``cython_version`` logic affiliated package-friendly

As reported in astropy/package-template#27 the logic for ``cython_version`` is not working for affiliated packages, leading to failures on Travis (not sure why I didn't see that sooner).

I'm marking this as critical, since it means that affiliated package testing is broken.

EDIT: I think no affiliated packages actually use Cython yet, hence why the issue wasn't spotted sooner.