For what it's worth, I support this idea. IC2 has a very high standard of inter-compatibility with other mods, and this change (which should be simple to make) would have a great impact in that regard.
Perhaps the easiest thing would be an additional parameter which disables the ore IDs, while the previous parameter would just disable the ore generation. That way people who use ore from RedPower, or wish to free some IDs, can still have them disabled.
To address concerns about the limited number of block IDS, having separate settings seems like the best of both worlds. Again, this should be very simple to implement.