I also have been working on this for some time and have yet to find a clean way to do it with PVS. Have you discovered any ways to do it?
Sounds like a very difficult issue. The first problem you are going to run into is when installing the agent it generates a unique GUID and since the Citrix Provisioning Server's Virtual disk can be shared this GUID will get duplicated which means multiple instances writing to the database as the same agent giving you conflicting data. The next issue since the drive is locked down you won't be able to write any log data to the Working Directory.
No idea how you could make it work, the only solution I can think of is to use SNMP and other external monitoring not sure how useful it would be though, maybe monitoring the host server would be a better more useful as this system would be pretty robust not being able to write to the system drive. Something to look into is what happens with the Eventlog data?!