Witchery is being disabled because it adds a lot of dimensions, and personally I don't think bundled with Galacticraft it's okay to have that many dimensions. So it will be disabled by default in 0.6.x. I will be releasing 0.5.11 soon which should have an alert (via YAMPST) warning people of Witchery being disabled by default.
Using the ore retrogen is pretty easy. Go to the cofh/CoFHCore.cfg and enable the option: B:RetroactiveOreGeneration=false to true. Then you will have to enable it for the ore(s), which are all located in the cofh/world/ folder. By default all ore entries have retrogen set to false. Go to the ore you want (sorted by Mod) and just turn config option: "retrogen": "false", to true. Then when you start up your world/server it will start retrogeneration of that ore in the world.
Cool thanks, that's really good to know. And as long as we have the option to keep witchery that's cool. Been using it a lot on my server.