Once we were satisfied with our changes we REZzed the files and had our patching software only modify the changes between the original and modified files. That meant that the size of the patch would only be a tiny fraction of the total files altered.
So I don't think that leaving the files unREZzed would have made the patch better, and anyone with enough determination and insight would still be able to unREZ them and tinker with them for them self.
But we'd be interested in hearing your ideas for modding the game. We had some ideas for an expansion, but MM9 never garnered the same devotion as the earlier games.