You're supposed to be stealthy in the game. IIRC if you're detected, you can't even fight back with your tiny krys knife even though Paul Atreides is supposed to be a prana bindu master. You're forced to stand around until your health is low enough to be able to do "the Voice" Bene Gesserit shtick which stuns the enemy. Then you can instakill them.
Now that I think of it, "Stolen" was another stealth game with such terrible design decisions. I finished that one too.