Stardew Valley, Kynseed, Sun Haven, Core Keeper.

Stardew Valley is just a planting-simulator. Has no story. It's just some infinity-game.

Kynseed is horrible sandbox-game, where your characters are constantly dying, and is just doing stuff for no reason aside doing stuff. I don't need this depression.

Sun Haven: why there is a snorlax blocking the way? _Also sounds weak on the story. But might consider.

Core Keeper is too pixellated. And you control a group? Nah.

Thx for the suggestions.

My advise is "My Time at Portia".
It hits not all of your criterias, but it's very close:

- the look of Graveyard Keeper -> nope, it's a 3D game and not a 2D Pixel game
- the limited amount of NPCs -> it has slightly more NPCs. They gave you quests/orders and you can relate to them, having dates and even get married (with one).
- the sandbox style -> yes, it is.
- the definitive ending -> more or less, it's not like in graveyard keeper, where you have the one goal and do everything to reach it. But you have some kind of main quest line and once it is done, the game tells you, it is over. But in my memory the game does not focus on it. You can even continue afterwards if you want and do an endless game.
- not so heavy on religion -> Once a week the people go to church, but you don't have to :)

I really liked that game and look forward to the next part of the series "My Time at Sandrock" (currently in early access).

And there is another game: "Travellers Rest".
It is on my watchlist (even before I played Graveyard Keeper), but it is still in development / early access.
I do not play early access games, so I cannot tell you anything about that game. But it looks nice and even GoG give me the hint, that this game can interest me, because I played Graveyard Keeper :)