How to calculate the amount charge transfer from a natural population analysis?
I will evade answering the main question because I am not feeling expert enough, but I want to point out that Natural population analysis (NPA) is very different (and better) from the Loewdin one. Loewdin is computed from orbitals of a special basis set (although it comes from the density, it is still free-atom-derived basis set which is used to obtain the density matrix). NPA (part of NBO) is from density matrix which is adjusted to the particular molecular environment, hence better representing the "real" atomic population. NPA is available in the commercial NBO program, old version of which is also included with Gaussian package (maybe also in other packages, I don't know). You can also try AIM charges which are absolutely basis-independent (if Your density is good enough). 

Personally I would think the analysis You proposed is fine with NPA or AIM charges, but I state again that I am not an expert in the topic. 

See https://www.q-chem.com/qchem-website/manual/qchem43_manual/sect0061.html and also http://www.huntresearchgroup.org.uk/teaching/teaching_comp_chem_year4/L7_bonding.pdf .