Best you can do is the dual install - it's been documented how elsewhere on the forum.
Essentially, you install the first, patch it as you want it, save the registry entries to a file, remove said entries, and install a second copy. Save the new registry entries to another file. Then load up the registry entries of the version you want to play.
I think it's somewhere around - local_machine\software\sonalysts combat simulations - or if you need the walkthrough search the forum for something like "beta dual install"
If you want to minimize the extra space used, you can junction the folders not modified by the patch - such as the world folder, and probably the audio folder. (Requires NTFS; which requires win2k or XP)
See
http://www.elsdoerfer.info/ntfslink/ for the software needed for that.