Yes, a penalty should be put in place for audience disruptions. In fact, people who laugh should be removed from the auditorium immediately. It is not fair for people at home to be unable to hear what is being said. Laughing influences how the candidates respond and should be eliminated.
Yes, some type of penalty should be put in place for audience disruptions during the debate. They are inappropriate and violate the rules set forth and agreed upon before the debate. The question is whether the penalty should be placed on the individuals causing the disruption or the candidates gaining the most from the disruption.
Any punishment would be more distracting than the original disruption. And if people knew that they might be punished for being part of an audience, they would be far less likely to want to participate. Eventually, candidates would find themselves debating in rooms empty save for the moderator and the camera people.
It is not reasonable to expect an audience to be able to suppress their laughter. Laughter is an involuntary response and it is totally unreasonable to expect people to be punished for doing it. All that moderators in a free country can do is to ask an audience to behave respectfully and hope that they do. For the most part. audiences in presidential debates are not rowdy and disruptive and they do not need to be regulated more closely.