I've never used GOG, but it seems to be a sort of Steam for older games. In that case, as long as it allows you to fully install UT GOTY you should also be able to install the M:R mod. Meanwhile, GOG.com does seem to offer a 30 day money-back guarantee so maybe you should look into whether they would give you the refund if you can't get M:R working. Again, if it allows you install the game proper, it should work with M:R.
: Is Marathon Resurrection the mod compatible with the GOG version of Unreal
: Tournament? I was thinking of getting it sometime.
: I've recently noticed comparisons with Marathon 1 and 2, and Unreal 1 anyway.
: (not the least of which being the starting fusion pistol)