Ah. OK. Answered by the author himself! 👍
My thoughts were:
It would be a risk to Stoker. While yes, she has a watch which means if he shoots her she won't reset when he resets time... There runs the risk of what will happen to Stoker.
Hugo has run out of bullets by the end of his dance and needs to reload, something the agents in the room would never give him a chance to do. And Miller was still positioned to kill Stoker. If he shot Dottie and she died, and time reset with her still being dead. Then we can picture Stoker being at Miller's mercy there. And if he is outright killed as a reprisal that's game over.
What Hugo does here is prove that he cannot out right resolve this situation on Dottie's terms. But he needs her to keep thinking one week by one week.
D-day is elegantly brilliant, and simple. Tomorrow we arrive at D-day.
So yes, killing Dottie is satisfying here, but wouldn't accomplish what he needs. And he is desperate to avoid hurting Stoker in the process.
He has, however, won a victory. Now to win a war.