We have the same issue: DoD requirements prohibit use of USB dongles. Since all of our virtual machines are 2012 we are unable to implement the already purchased system. Also, we can't use the cloud version since all of our stuff has to reside within our network.
New releases of MediaServer should be without dongles - after all a dongle an outdated security solution.
The question is when will the new generation of MediaServer be available and will it be more in line with current security trends?