By design, Munki bundles all updates, installations, and removals to be done at once—either by the user through Managed Software Center, or by Munki in the background once every hour or so. There may be some exceptions in the background (for example, if there are blocking applications), but to the user interfacing with Managed Software Center, it’s either all or nothing, and that’s by design. Greg Neagle, Munki’s primary developer, refers to it as a carrot and stick approach, which basically encourages users to install updates by saying “Hey, if you want this piece of software, you can’t keep putting off all your pending updates.”
I don’t think it’s quite that simple.
On the one hand, yes, if you allow users to easily install and remove various things while ignoring pending updates, that makes it very easy for users to ignore pending updates. On the other hand, if you want users to “buy into” how great Managed Software Center is, you want to give them the impression that MSC is there to make their lives easier and not more difficult.
When I have a user who says “How do I install this?” and comes to me with several pending updates, which I know won’t be quite installations, I try to gauge the urgency of this installation (and maybe ask the user, too). If it seems the user has time to install those, I’ll encourage her to do so. If it seems like a rush, I have a workaround, which is to have her click INSTALL next to the item she wants to install, and then I launch up the terminal (switch users, if necessary—or ask the user to enter her password when prompted):
sudo managedsoftwareupdate --auto
This basically does the background run that Munki already does every hour or so, so if there are updates that require a logout or reboot, those get temporarily ignored, same as updates that have blocking applications.
In addition to encouraging people to install updates when they do have the time to do so (aren’t rushing off to class right away), I do also force updates occasionally. It’s not ideal, and I wouldn’t recommend to do it very often, but if you never do it, you will have faculty/staff/students who basically never install updates. Be judicious, though. You know the culture of your school better than IT folks at other schools do. Could you get away with forcing it every month? Or is once a twice a year more likely to go over well with faculty?