Long silence after my post, my bad. Anyway nix=delete, get rid of, flush down the lou. I'm sure there would be away to fix it, but given that the nether ores doesn't add that much content, I personally didn't see any reason to bother. However, if running mocreatures with more mobs in the nether, then i could see a reason.
I like to push for simplicity, rather than complexity, which is why I just flat out dropped nether ores. Everything else plugged in no issues. Also, with tekkit, I find more interest in BC, IC, and RP, and all of that can be fully experienced in the overworld, with only a short trip to the nether for glowstone.