as the error message says, there is a bad conflict on the GEOS library. that said, it's more or less like finding a needle in a haystack.

my personal experience about Python is practically nothing, and I have no idea what Shapely could be; any kind of debugging is practically impossible.

hint: try using a newer version of SpatiaLite (as e.g. the very recent 5.0.0). several things have changed in the meanwhile about the iniatialization of GEOS.