One thing that I was wondering: would we be fine with also writing some things in Cython instead of C (especially things that would not use the ufunc machinery but need to written more manually) ?

Some things (eg the shapely interaction I was doing in https://github.com/caspervdw/pygeos/pull/47) might be simpler to do in cython.
On the other hand, that creates more different ways to do things, making the library as whole more complex.