All of which is to say that universities, even public universities, are not government entities in the same way that public schools are. It is far from clear to me that libertarians would support the idea of a private citizen working for a non-government organisation being compelled to hand over private communications by the government.
Of course I might be wrong about UVAs status, but I did a fair amount of searching, and could not find anything that would indicate that university employees were in fact government employees, and the information that I did find tended to support the idea that they were not. If I'm wrong about this, then the OP's position is easier to understand...
Since UVA employees's salaries are publicly available through FOIA (see http://datacenter.timesdispatch.com/databases/salaries-virgi...) I think that's one pretty good indicator of civil service status. In Virginia, the University is required to report salary information, etc, to the Virginia Department of Human Resources Management. They are able to adjust how they report salary information for employees who are paid a portion through endowments and other outside sources.
Now, I have no idea or information about the specific case with Mann - who knows, maybe he was being paid exclusively by some special endowment and so his records would not be subject to a FOI request - but I would have thought they would have used that in part of their justification for not complying with the request.
Also - I don't consider myself a libertarian so I won't speak for them - I'm just a big proponent of government transparency.