It's different because Wolverine believes Daken can be saved, that the reason he's like this is the product of his upbringing/Romulus' machinations. And The Cuckoos have proven that they are capable of thinking for themselves, and as such whether they were built to destroy the planet or not it does not appear that they will.
The case with the Scarlet Witch however, at this point, is being said to be pointless. Xavier, the world's most powerful telepath cannot help her with her issues, and he says that he cannot control her dangerous and rapidly fluctuated powers. Strange also says there is nothing he knows of to help her, and so we are being shown a case where all possible attempts to help her have proved fruitless and for the safety of the world she may have to be killed. Wolvie and Emma rather callously go about putting it out there, but they really aren't wrong to do so in this situation, nor is it hypocritical of them to not consider it in the case of their own children.