My Gems (and the Emerald) WILL be exchangeable in Redpowerrecipes (except the basic Tools), so theres absolutely no Reason to have RP-Gems, and i hope Eloraam will nerf the Gemamount, or at least add a Config to disable them as they are extremly OP.
Couldn't you simply disable RP gems usage for recipes from your addon, and leave them other way ? Because they aren't OP (mainly because they are a bit useless with IC² except at te beginning) but too common for being used as something that is about as valuable as Diamond (Ruby is a bit less valuable, because it can just replace diamond in Energy Crystal recipe, but Sapphire can be seen as a way of saving 1 Diamond + 8 Redstone, even if you cant use it for crafting a Diamond Drill). And if you don't want RP gems being useless, make it usable to craft Gem-Armor