Hope you're feeling better.
I think you've correctly called it on what's going on with Cipher. It didn't occur to me but when I watched last episode's reaction and you said it, I thought that has to be it and I think this episode almost confirms it. Especially the feeling pain the whole time thing.
I've got to think that Cipher/Godolkin is planning on somehow using Marie's powers to restore his old body.
I did prefer S1 I think but I have to say that Hamish is single-handedly making this season unmissable.