I haven't played Phantom Pain yet but I've played Ground Zeroes and I simply must play the mission non-lethal. Why you ask? Well, the two guards at the front gate themselves don't even know who Skull Face and XOF are, let alone what they are doing there. As far as I can tell they're just some random US Marines tasked with guarding what they are told are terrorists ("enemy combatants" as one puts it). One conversation between a couple guards shows that even they're uncomfortable with how locked down and intense the base is becoming. Yeah, they're not civilians, but they're just doing their job aren't they? Remember in the tanker mission of MGS2? The only enemies you were allowed to kill were the terrorists that took over the boat. The marines listening to the Metal Gear Ray speech were to be left alone and simply avoided (partly because there were so many of them! haha)
Try to answer this as best you can without spoiling anything please. Does the Phantom Pain pit you against more deserving enemies like the Cipher group and XOF soldiers or is it more of this morally ambiguous fighting against everyday grunts?