Any way to free the mind controlled soldiers from the spell of those three wizards, or is killing them the only option?

Unfortunately, you have to kill them, there is no way to free them.
You do end killing the mages who cast the mind control spell, but it's much later in the game, and I don't think it would do anything, even if you kept the soldiers alive until then.

Ok thanks.

An unrelated question- Does anyone know if the traps skill was toned down in the GOG version? I remember traps were absurdly overpowered in the original version, especially death scorpions.

GOG doesn't add any gameplay changes to games, only makes the last patched version compatible with recent OSs, though they usually provide links to unofficial patches/mods for games that have them.
So the overpowered scorpion traps are probably just as bad, though I haven't tested this myself, since I played an almost pure mage with this version.

I recall bugfixes for skills as well as toning down Death Scorpions from the patch here versus the one that is available for people with the boxed version of the game. There should be a readme with all of the patch fixes in the game directory.

I just checked the readme, and it does mention that Scorpion Trap is less powerful. Thank you. I was afraid that it might make the game too easy, but I'll guess I'll try it now.