Source: scipy Followup-For: Bug #1020561 We could consider creating a pythran-free build of the package, providing an alternative via Conflicts/Replaces.
As you noted, it would require some effort to get the management of the alternative build in place to run alongside the default build. But it can in principle be done. It would possibly want to be done with a python3-scipy-common package dependency containing just the plain .py files separate from the compiled .so extensions.