Argent brings up something very interesting here. What if Harmony cant do the most logical thing? The best possible course of action would have been "Hey, Wax, I need you back in Elendel. Your uncle is up to some shady stuff. Oh... and your girlfriend is a kandra. I sent her to protect you."
What if that was impossible because his shards were in conflict? That puts everything in a completely different light to me. If he did all he could do, then yes, this was probably the best course of action, if he could have told Wax, but didnt, then no, then he screwed up.