He's saying it because he realizes that she is a copy of Rachel, not the real Rachel. No matter how hard they resemble each other, it's not her. Even if the eyes match, he would have found something else that reminds him that they are not the same.
In saying so he knows that the (copy of) the woman he loved will be destroyed. This shows that he puts the safety of his daughter above anything else.
And it's a jab at Wallace's Hubris. He may think he's a god but he can't duplicate Rachel.