Warren had already begun to question whether what she had with Cooper was too good to be true. There was foreshadowing that something isn’t altogether square about the two of them, the talk about one being dead and the other—when Cooper says he’s definitely alive.
I think with hitting Cooper, fighting him physically, Warren was drawing a line. If you hide something from her, try to keep her from her path, her friends, etc., it’s over. He knew exactly who Murphy was and he still tied him up and put him in the trunk. (The battle in between-loving and still not trusting—is a fight she will walk away from. And yet, she did not kill him.) She’s been there and done that. She also seemed to not want to know what Cooper knows about her—she shut that down quickly.
I think he will pop up again. Interesting too, but totally in character, she blows off Murphy’s questions about who Cooper is. I also imagine that fighting him, hitting him, is an attempt to get him to stay away, to not pursue. It’s like once Murphy showed up, a flip was switched. But again, I think Cooper may just make his way to Newmerica.