Except that he wanted to kill Kirk before that, and he wanted to kill him afterwards. It may not be a plot hole, but it could be considered out of character considering his actions everywhere else in the movie.
I find it perfectly consistent. Throughout the movie Khan struggles to make effective strategic decisions when confronting Kirk because he lets his emotions overwhelm his judgement. One time he pulls back when Kirk taunts him, believing that he could let Kirk die without risking another costly confrontation. (Khan doesn't know of the Genesis cave (a dead end anyway because of the protomatter) and believes he has the opportunity to hunt down Enterprise.)) The next time, he lets his rage take takeover, following Kirk into the nebula after he is taunted. It's not an issue of Khan changing his mind; it's a matter of him making two sides of his personality--one logical, one violent--canceling each other out.