My customer has invested a large amount of money in their existing SCCM/App-V infrastructure. When working on new VDI deployments, I emphasize re-using existing infrastructure when possible, to save costs and shorten deployment timelines.
Having the SCCM Agent and the App-V agent installed on a VDI master image is not always desirable, but it can be done successfully. Here are some links that I found useful:
Problems with Sysprep not reading the App-V Q:\ drive (Includes a simple .bat file solution):
http://tech.zsoldier.com/2010/03/view-composer-agent-initialization.html
Manually Uninstalling / Installing SCCM Client (it's not hard, but it is all command line, no GUI):
http://technet.microsoft.com/en-us/library/bb693546
Preparing a Master Image with a pre-installed SCCM Client:
http://systemscenter.ru/smsv4.en/html/d34f1195-ffad-4e7b-b302-5df64d373710.htm
