Sticking with python maybe scons would be an alternative? xmms2 uses it - while they are friends of mine that I have a lot of respect for, technically and otherwise, I still believe that make is good enough at dependencies. :) May just be inexperience though. http://www.scons.org/
I just gave a brief look at scons and I like what I see. Need do some more reading on how we would it use the existing python config setup we have. This would at least remove all makefile magic without adding any extra dependencies.