Honestly it seems like a really good mechanic. With an investment of 450 lapis, it becomes slightly better than normal ore-doubling machines, but there are drawbacks that make this balanced. First, and most importantly, you have to manually mine stuff. Ore doubling machines (including the old RM Furnace from EE2) can easily be automated, while this requires constant manual mining. Secondly, mining with fortune (esp. compared to silk touch) causes inventory space to run out faster.
Still, you shouldn't be forced to disable a feature of your mod just because of another mod adding a conflicting feature, just as he shouldn't have to entirely disable his feature. I've suggested to him that he ought to create blacklist functionality so that when other mod authors make smelting recipes for getting back base materials, they can easily add the block to a TC blacklist to prevent TC from fortunesmelting that block.