From my limited experience, NPCs come in two varieties, persistent, and instanced. An instanced NPC is a bandit on the street who, if you kill, will drop loot, and then never affect the game ever again. They appear and disappear as easily as a glitchy texture. A persistent NPC, you will probably want to track more of, but even then, you don't have to track everything.
A shopkeeper, you may generate their shop inventory when the player loads the area, but then clear it when the player leaves the town, or a certain amount of in-game time has passed. Same with aggression responses, you could have a list of NPCs who are unhappy with the player, and after a while, they're removed from that list. No need to store the NPCs dynamic opinion on each NPC, just that they are unhappy and when from. When you load the area, you check that table, and the NPC reacts accordingly.
Maps, you'd want to do region by region too. Of course you'll need your data files, terrain, navigation maps or whatever you need, but for the most part, you can choose to only store changes. This means you don't store the whole region in a file, only which containers have been looted, what persistent NPCs have been altered (enraged, seduced, quest actions completed) and such like.
Player stats... yeah, surely you need to just store those in the save file and assign them to the player object. Level up, when you reach the level up conditions, you get to improve. How that works is entirely down to you, the dev. Don't be afraid to play around and see what works.
I'm sure there will be other people with far better advice, but this should help guide you in the right direction.
There's a lot of reasons why people will respond negatively to someone deciding to excise themselves from reality, and part of that is because there are a lot of different types of people, but we're almost all of us inherently social creatures.
Some people may feel sad that the person who ceased to be didn't think to reach out to them, or didn't clarify what was going on. This often comes with a strong feeling of guilt, a feeling that the former individual was let down by their friends who 'should have seen the signs'. The signs can however take many forms, and be easy to miss.
Some people may feel that life is so amazing and wondrous that's a straight up insult to discard it. Anyone doing so is almost invalidating their optimism, and it feels like a personal attack.
Yet other people, much like the first group, will feel like they were indeed given up on, like they weren't given the chance to support the no longer present individual. A slightly different perspective that can feel like disrespect.
Finally, there are people who don't want to acknowledge the option even exists, and anyone who uses it is making it more real. We want it to be so last-resort, that it's never considered an option.
At the end of the day though, it's always a permanent solution to a temporary problem, no matter how big. If you're really considering it, you've spoken to the helplines, tried to get the support of all your friends and you're out of ideas, sell all your shit, hitchhike 3 states over, and spend 3 months trying to live there. You literally have nothing to lose, and it's worth trying every fix before making what is literally the last decision you will ever make.