I think what you're doing now is fine. I would add, do not mention or bring up their stutter unless they do first. Additionally, waiting for them to finish speaking and not interrupting them is definitely the right thing to do; some people here may disagree but I would add that if (and only if) they seem to end their thought without completing do to struggling, it may be appropriate then to gently suggest a thought if you understand the point they were trying to get across. Just to keep the flow of conversation going (and to show them it doesn't bother you and you are actively listening).