After you kill the guard in the prologue, Michael literally says "You didn't have to to do that" and later in the game the number of bodies at the bank job is referenced. Is there an option not to kill the guard?
It appears that you HAVE to take out the guard no matter what.
As shown on this website you have to take out the guard. So, it appears that he is just saying that "You didn't have to kill him" as a on the spot remark when there actually was no alternative.
Further proof is shown here:
Michael is held at gunpoint by a security guard who removed his mask covering his face and is later shot in the head by Trevor.
I'm a little late, but being wrapped up in the Karma conspiracy, I wondered the same thing.. I tried multiple ways to get passed that prompt without killing that guard. If you shoot him in the leg, he falls but shoots Michael in the head. If you try to shoot his hand or gun, you end up shooting Michael in the head. I have a theory as to why you are forced to do this, but I'm very interested if anyone finds a way around it!