It's not a Cython issue per-se -- you can't reload compiled extensions at all.
Can you find a way to cache the data / store it in a more compact efficient way to make loading it faster?
Final kludge -- I think pyximport does a hack where it doesn't actually reload a module, but rather, loads a new one, and "hides" the old one. This means that if you did this for along time, it would keep piling up a bunch of old modules, but a few exrtras lying around won't hurt.
So you could do a similar kludge, or maybe use pyximport:
-CHB