PyPy doesn't compile ctypes. It compiles rctypes, a subset of ctypes. As long as the SDL module is only declaring structures and C functions it should work.
Sorry I wasn't clear on that. Also of note is that (like everything in pypy) rctypes is under heavy development, especially the static translation aspects of it. There is a decent amount of code written against rctypes by now thanks to a couple Google Summer of Code projects to build up the standard library for PyPy.