What I meant in my question was “How much of a moral variety do you allow in the PC in any given game?” and “If the PC can take actions that are reprehensible to your personal moral code but not frowned upon in the game, would you let them?”
I hope that clears things up!
the MC i’m making can do terrible things “for the greater good”.
The MC in my game is a statesperson so the “good” or “bad” are very morally grey lines, still i don’t know how much “extreme” measure can i let my players take without making my game enter the “mature” rating or pull out to many punches and don’t let the player play the game at his fullest.
Generally, I don’t have a problem with the reader playing their character as bad/evil/mean/selfish/whatever in my games, though there’s a few things I won’t allow.
I just have no idea how to actually write characters like that. 
How do you write POV characters whose motivation you can’t empathise with?
Usually, the characters in questions don’t see themselves as mean/selfish or evil. All you need to do is to figure out how they see themselves, which might be very different from what is actually happening in the world. The POV of the main character doesn’t have to be right or true, it just has to be internally consistent.
Mistborn Series Spoilers: The lord ruler is a PERFECT example of this. Throughout the books you think this dude is awful, what a monster. But by the end, you’re like, oh crap, maybe we shouldn’t have killed the guy holding together the fabric of reality. Yeah, he executes people and keeps everyone in slavery, but I mean, they’re alive.
Like any other character. Often they have good justifications for what they are doing. A solid reasoning and a goal in mind . They have faith in their skills and their path and whatever wrong they do…its collateral damage for their vision of ‘greater good’’ or whatever .
And that is fine for me when I’m writing NPCs, I can kinda distract from the mental disconnect because I know — in an intellectual, abstract sort of way — that people can have motivations, defense mechanisms, and behaviour patterns that doesn’t make sense to me. In a way, they don’t have a choice, because that’s who life has made them into.
I just find it much more difficult when it’s the PC, who is both the pov, and a character who isn’t set, who does have a choice. It probably sounds ridiculous, but I just sit there, stuck on how someone is intentionally mean, and my brain objects when I try to understand it, make it make sense to me.
Maybe it’s because I’m not the one deciding their motivations?
Think of it like this…
Lady Luck look at the table and before her are an assortement of cookies and baked good .
1- Pick the strawberry cookies! yum yum
2- Pick the chocolate Cake! A slice made of heaven!
3- Pick the Vinaigre cake, with slice of citrus…Yurk.
Now you probably gonna go for chocolate right? But you don’t get to say ‘‘no no no!! whats wrong with you!! Vinaigre…GAG Urgh gross’’
Just write it lol like any other choice . You can muse about how anyone could pick that choice…in your insomnia induced night 
well you do give them, so to me from my side…over here . Seem like your brain go TILT cose its trying to reason and think about someone else brain process .
I wish I could just write it! 
It’s not so much how people can get themself to do it, but more how to actually do it? If that makes sense? How do you intentionally hurt someone? What do you say?
My brain just go into blank ‘error’ mode when I try connect with it emotionally, and apparently I can’t write a pov character without doing that?
When I do manage to write something, it just sound weird and forced to me, and my editor brain wants me to delete it because it’s ‘unrealistic, bad writing’.
(I should probably note that my brain have a tendency to get stuck on blank in other situations, where it’s trying to find the ‘right’ answer, and there either aren’t one, or I’m missing some of the data required to figure it out. A lovely little side-effect of my personal mix of autism and anxiety…)