Changing the domain of the ACS erver to a different domain from the user domain should work, but there are caveats.
You will have to make sure there is a trust relationship between the two domains. This may already be the case in your environment.
There was also an advisory published about ACS 3.0 with Active Directory user authentication.
http://www.cisco.com/warp/customer/770/fn20228.shtml
If you can not get passed the workarounds outlined in the advisory, then your best bet is to go to the most current release of ACS.
Marcus