It's not perfect, to be sure. To credit Konami with intentionally making combat obnoxiously clumsy is a stretch, and the entire scenario above could have transpired simply because I am amazingly bad at playing MGS. But it's not hard to see this was what Kojima was trying to get across. Snake's own role as the reluctant hero, elaborated in Codec conversations and storyline moments, very clearly illustrates his distaste for unnecessary killing, and Liquid Snake even goes so far as to accuse Snake of enjoying gunning down enemy soldiers, just to get a rise out of him. Kojima intentionally uses everything in MGS - from the memory card to the back of the CD case to the Dual Shock controller - with the intent of telling his story, so it would be uncharacteristically inconsistent of him to not keep that in mind while designing the gameplay itself. But MGS is still too crude to articulate any of this very well; to a certain extent, it feels like the player has no real choice quite yet.
So, from here, we proceed to Metal Gear Solid 2: Sons of Liberty, a game which managed to piss off all the newly created Metal Gear Solid fans by giving them a whiny bishounen punk kid instead of the beloved Solid Snake, and telling a story that is half spy-thriller and half love story at the same time. Perhaps the greatest improvement MGS2 had over MGS was a combat system that didn't suck; thanks to additions like a first-person combat view and localized damage, killing was easier than ever. However, we also had a new weapon at our disposal, namely, a tranquilizer gun that works on everyone, including bosses, meaning, for the first time, the player was capable of getting through the game without killing a single person. Unlike MGS, attaining the highest end-game ranking ("Big Boss") required the player kill absolutely nothing throughout the entire game.
But if MGS gave us too strong an incentive to avoid killing, MGS2 ditched the incentive altogether. Sure, hardcore Metal Gear Solid fans will most likely rise to the occasion, but the average Joe or Jane is probably not going to even bother playing through the game a second time, and will have had little to no idea they were ever supposed to avoid killing people. Where MGS may have been too heavy-handed, MGS2 wasn't nearly heavy-handed enough. The same do not kill theme was in there, but it was buried underneath a plot full of weird. It didn't do what MGS did right - that is, tie the theme directly to the game. Instead, the incentives to avoid killing were virtually irrelevant, if you don't care about rating or collecting all the dog tags.
Last comes Metal Gear Solid 3: Snake Eater. Unlike the first two, the game's balance and pacing was heavily inspired by action movies, and as such, it was perfectly reasonable to play through like Rambo. The rewards for using non-lethal means increased, though; in addition to requiring zero kills for a Big Boss rating, each of MGS3's bosses only dropped their trademark camouflage items when you knocked them out. Perhaps one of the most significant moments of the game, however, pitted you in a boss fight against a long-deceased psychic named The Sorrow, who had the supernatural ability to communicate with the dead. This haunting "fight" took place in a ghostly jungle river similar to one the player had traversed earlier, except this time Snake was forced to wade upstream, dodging bullets and encountering the ghosts of every single life he took, ranging from jungle animals he killed and ate to gruesome shadows of enemy soldiers who recount exactly how the grisly deed was done. And, despite his extensive arsenal and elaborate hand-to-hand combat training, Snake couldn't fight back - all he could do is continue upstream and do his best to dodge the ghosts of his past. This was no minor segment, either; should the player be fairly indiscriminate in his killing, it could take upwards of 20 minutes to complete.