yeah, the game is SUPER finicky as to where exactly you can preform the kill... it can be done, but yeah I ran in to a similar problem several times that depending on where I made the kill (even though I was "completely out of sight") killing the eye in certain places causes one of the Duergar to go investigate and that is when they turn hostile, but I agree it makes no sense since there isn't exactly a body to find...
Being forced to save scum over things like this is just bad game design.
