Never recall him wanting to take the Emperor alive. I doubt he even considered the Astronomican or the Dark Gods told him they would sort that issue out.
Custodes and Wolves? I imagine he had every intention of killing every last one of them. He would never have assumed the Custodians or Russ would give up and serve him, he would know that every single one of them would die before turning on the Emperor. Same for most of the other loyalist Legions. I say most as he seemed to believe both Ferrus and the Khan would side with him.