That was one of the things that made The Matrix so special: it's bizarre mixture of references to religion and mythology.
Yes, you had the christian and jewish references (Zion, for one), as well as greek mythology (nebuchadnezer), roman mythology (the oracle of delphi), buddhism, cyberpunk and - most importantly - a little bit of Lewis Caroll style wonderland philosophy (Follow the white rabbit).
It was this mix that brings the story to life, and I can't imagine how much an edited version could mess that up.