Several pieces of hopefully not unfounded good news:
The pdflatex and dvips tool chains both support suffix-less includegraphics filenames. In fact, the pdflatex version pretty much requires them (otherwise it bails with the first missing graphic, which breaks dependency generation). So, using includegraphics without suffixes should work properly in both places. If a file with a known suffix is not found, the makefile will try to build a pdf from any suitable file it can find.
The second bit of news is that the makefile knows how to build pdf from eps, so things should just work. If, after removing suffixes from graphic includes, things don't just work, please file a bug at http://latex-makefile.googlecode.com/ and I will look into it.
I want this to be as painless a transition as possible for everyone.
- From my Nexus One: watch out for spell bumps