Okay, I just tried something and it seemed to work.
The unofficial patch's readme says it keeps the original executable intact:
"To play the updated v1.40 version of the game, run M2V140.exe from DOS or DOSbox. To play the v1.31 version of the game, run Orion2.exe."
...unfortunately, the Orion2 supplied by GOG seems to be a renamed m2v140.exe, or at least, it was patched as well.
So here's what I did to revert Master of Orion 2 to the last official version, and, as an added bonus, also generated the latest unofficially patched version as well:
1) Install the GOG version of MOO2
2) Download moo2v131.zip, the last official update patch. I got mine from here:
http://www.fileplanet.com/159032/150000/fileinfo/Master-of-Orion-2---Update-Patch-to-v1.31
3) Rename Orion2.exe to orion2.exe.bck (to keep a backup of your default GOG executable)
4) Extract the Orion2.exe from moo2v131.zip to the Master of Orion 2 directory. (e.g., C:\Games\GOG.com\Master of Orion 1 and 2\Master of Orion 2).
Now you have MOM2 v1.31!
For the latest unoffical patch, which can be installed in tandem with the official version:
5) Download the Moo2 v1.40b24 patch from here:
http://lordbrazen.blogspot.com/2005/01/download.html
Extract the patch to the Master of Orion 2 directory, then follow the patch's installation instructions:
How to Update to Version 1.40
*****************************
1) Download the updater file named "MOO2V140.EXE" Please be
sure to note which directory you download the file to.
2) Copy MOO2V140.EXE to the Master of Orion II directory on
your hard drive. This directory is usually \MPS\ORION2.
3) To update your copy of Master of Orion II to version
1.40, simply run the MOO2v140.EXE. It will create a
separate M2V140.exe
4) To play the updated v1.40 version of the game, run
M2V140.exe from DOS or DOSbox. To play the
v1.31 version of the game, run Orion2.exe.
,,,,So now if you want the original 1.31 version, run Orion2.exe. For the lastest unoffical patch, run M2V140.exe. And for the Win95 version, which was always v1.3.1, run ORION95.EXE.
Hope this helps!