I think at that point, Logan wasnt overly thinking about what Rhodes would do if he found out what he did to Nicotero. I think he immediately severed the head just for research, threw the headless body in the freezer, and didnt even consider the consequences. Things were getting pretty tense by that point, and Logan was on the verge (or past it) of losing it. Even if Nicotero did rise, Logan should have been able to control him ans sever his head, because somehow, he had managed to control/experiment on the other specimins. It was always weird to me that he was working by himself, with no military guards in his lab to protect him/his work. Maybe he was a secret badass, we just never get to see that side of him.