I would suggest not to provide GoToMeeting through Munki. When I did, I found myself with the same problems as you, and a lot of complaints from users. About a year ago I discovered that users could download the correct version of GoToMeeting just before the meeting began, and run that version from their home directory, without requiring admin privileges. So I removed GoToMeeting from Munki, and instructed my users to download and run it themselves, and I haven't heard complaints since (apart from the occasional 'why is G2M not in MSC'?). Your users have to be allowed to download and install the client in their home folder though.
Another option is to have your users use the recently released web-based client (I think it's officially called the 'GoToMeeting Web App'). One of my colleagues tweeted a few days ago that it worked quite well.