I'm also sort of unsure on this one. On the one hand, the TC feature is well balanced with itself (anything that is smelted is pretty much impossible to get back, baked potatoes can't be planted, nor can cactus green, glass is destroyed when broken, etc.). On the other hand, GT is using smelting as a way of getting stuff back (which isn't uncommon in mods, but most tend not to do it with blocks).
I can understand mDiyo's response that "Greg's fault, Greg's fix", as that seems to be a trend among the devs now. If GT breaks something, complain to him. On the other hand, this isn't going to result in GT removing the smelting recipe. The only outcome I can see is for the smelting/fortune module to have a "blacklist" of blocks that aren't applied. If mDiyo isn't the one to implement it, Greg will likely just steamroller over his code and be done with it.
To be honest, it's a bit childish, but I suspect that it's not the only issue that's at the cause.