This was the ONLY method that worked for me:

Find jasp.exe,
Right click,
Create shortcut,
Right click on the shortcut,
Go to properties,
Copy and paste the following into the target line, your exact path may vary,

"C:\GOG Games\Star Wars Jedi Knight - Jedi Academy\GameData\jasp.exe" +set g_sabermorerealistic 2 +g_dismember 100 +cg_dismember 100 +helpusobi 1

Why is this necessary? The new releases include a patch which has this mode write protected in the settings. With this, you can play the game as it was meant to be played with full dismemberment. If you change set g_sabermorerealistic 2 to 3, the lightsaber is deadly at ALL times. That means idle animations, death animations, etc. I also recommend the cheat, "iknowkungfu." That adds Kyle's special melee style for the player to use, as well as maxes your force powers. That can be turned on with either helpusobi 1 or devmapall.

I use the following autoexec:

seta helpusobi "1"
seta g_sabermorerealistic "2"
seta g_dismemberprobabilities "0"
seta broadsword "1"
seta g_corpseRemovalTime "0"
seta g_dismemberment "3" // 0 = no dism. 3 = allow all

// multiplayer
seta g_dismember "100"
seta cg_dismember "3"


What I can't find anywhere is what does g_dismemberprobabilities exactly do? Some say set it to 100 others say set to 0 to dismember every time... I have it at 0 but I can't see any difference. Some NPCs will never dismember at all with this set to either 0 or 100...

The "g_dismemberprobabilities" maybe not works on version 1.01 and was replaced with an another command. It is do the same as the realistic combat, but it do no death blows. So your opponent will be dismembered only if they die from the blow itself. But not even with 100% probability.

For posterity: Quoted from here

This didn't work for me either. Something else did however... I'm not allowed to post links (really, GOG?), so here's the workaround link:
(DOUBLEU DOUBLEU DOUBLEU) (DOT) pcgamingwiki (DOT) com (SLASH) wiki (SLASH) Star_Wars:_Jedi_Knight_-_Jedi_Academy#Enabling_full_dismemberment

...and here's the text in question:
"
1. Navigate to <path-to-game>/GameData/base.
2. Create a file called autoexec.cfg in the same folder.
3. Add the following lines.
helpusobi 1
seta g_sabermorerealistic 3
seta g_dismemberment 3
seta g_dismemberprobabilities 100
seta g_corpseRemovalTime 0
seta broadsword 1
seta g_dismember 100
seta cg_dismember 2
seta g_saberRealisticCombat "1"
Notes

Works for both single player, as well as multiplayer.
"broadsword" sets "soft bodies" (rag-doll physics).
0 (disabled), 1 (enabled), 2 (enabled and skips death animation)
"g_sabermorerealistic" sets the "sharpness" of the lightsaber.
0 (normal), 1 (higher damage), 2 (cuts parts off when damage is fatal), 3 (even touching the blade kills instantly)
For GOG.com version use version 36513154 when installing the game.
This commands do not work when starting a new game, you must first start a new game and then restart the game continuing your save file in order for this commands to take effect.
"