i don't think it's false sense of accomplishment at all.
yes, history will see him as villain, but, for example, at the start of metal gear 2: solid snake (iirc) it is said that there are no more nukes left in the world other than in zanzibarland, and while not explicitly stated so, i think dd's nuclear disarmament efforts in mgsv contributed to that - at least there is a cinematic in mgsv for total nuclear disarmament, which makes it canon enough for me. that's a big accomplishment that matters, imo.
it's really futile with the water reservoir and, mb, the child soldiers, since we don't know whether they got a chance at "normal" life (and it was miller's idea anyway) and know the fate of liquid snake and kids transferred to outer heaven later.
in shining lights mission he prevented a dangerous infection outbreak. like with many other things, it can be argued that he is responsible for it happening to begin with.
for me personally it is an interesting question how much of all of that did big boss - both ishmael and ahab - really want and how much was he being guided and/or manipulated to do, or left no choice. but i think the thing with playing as venom snake is doing the right thing at every given moment, even when war has already changed and is for money and revenge instead of making world a better place like the boss or ishmael wanted. but venom snake loved the legend of big boss the hero before becoming venom snake and my guess is he continued to do so and was happy or at least accepted the chance to contribute to it and become its co-creator. he contributed to the reason to live of his staff and completed impressive missions, and while that might seem shallow and lacking a bigger purpose, to me effort and passion in itself are never meaningless.
one can say that he has no lever and everything was decided for him, and that makes sense. but also it would be easier to give up or mess everything up; he needed effort and willpower to keep the tram moving, even if there was only one path - whether willingly or not and happy or not seems to be up to the player to decide.
also lmao, there was never a "good" option and non lethal metal gear gameplay is a joke. in mgs3 bosses even explode anyway, i think the only difference is difficulty and a little trophy to let the player feel like a good boy/girl/them. it is a game about supernatural cyber war and the very essence of all of your efforts (warring) is inevitably bound to people being killed. the closest to genuine non lethal i know is total stealth in mgs1 where at least the genome soldiers you sneak past are not even bombed in the end.
Playing MGSV:TPP you have 2 choices:
You can be good or bad. You can kill, destroy, use and do everything in your power to be the worst person alive. You can be kind, you can save animals, kids, soldiers, grow a family and be a respectable man.
There's actually no choice. There's no two-tracks. The ending is the same. History will see you as a villain. You are a villain. You are, currently, the perfect depiction of the most wanted and most evil man alive, according to the world.
You have no lever. You cannot stop this from happening. Either close your eyes or watch, the ending will be the same. Your life will end in misery. The only relief? Boss will pat your shoulder and let you die with a false sense of accomplishment. Congrats. That's the panthom pain everybody talks about.