ADS and VMs need to coexist. How?

ADS and VMs need to coexist. How?

I work for a university and we are currently tasked with setting up a new
computer cluster. That is like breathing for us, it is so easy. This
cluster though is special. It will be shared between 5 different
departments. Each department has their own licenses for software, custom
settings, and specifications. This has led us to the decision to use
virtual machines for each department and just have a shortcut on the
desktop of the host computer to each. This was mainly chosen, because we
already have images in place for each department so making a virtual
machine is super easy, no need to build one from scratch.
This wouldn't be so hard if it was just left at that, but further
complicating this is the fact that we run on a Windows Active Directory
network with Windows computers. If you are unfamiliar with active
directory, basically it is just a big login server that keeps track of
everyone and their stuff. That being said, many of the applications that
we run require a specific user to be logged in so that it has access to
their user profile. This is dumb I know because whoever developed these
programs didn't have to install them across a university. With active
directory each computer on our network is joined to our "domain", which
allows us to management them without going to each and every computer.
Now we are talking about 50 computers here and 5 virtual machines on each,
joining them all to the domain is simply not going to work, because we
still need to be able to easily update them when departments want more
software. But we need to have the users profile available to the virtual
machine so that they can use the programs needed. This is easy if you know
exactly who is logging in, but we would have to rely on using the
environment variable to see which user profile to mount into a generic
profile on the virtual machine.
So my question is pretty broad, but is there a better way to do this that
we just aren't seeing?
Also, is there a way to tell vmplayer to mount the current user's profile
only?
I hoped I explained well enough, but if you have any questions please ask!