Has anyone played a violent game with battles and such that actually made you regret some of your decisions to kill? And I don't mean because that one npc would have had a great reward for you later on. 
the only game that even begins to come to mind is Dishonored , and that one doesn't really make the merciful options seem merciful
in fact , some of the non lethal options seem far worse than any of the lethal options
but this isn't really the case of finding a non violent solution
I don't really remember any game that gives serious non violent options , or focuses on a non violent gamestyle (I know of games like Thief and games with a similar formula , and I believe Hitman is the game you mention where you are penalized when killing innocents , but I never played these so I can't speak from experience)
if such games truly exist , I don't think I've ever heard of them
Elder Scrolls Online penalizes you if you kill civilians or steal from them, but it's not an altruistic feature: it is part of the Dark Brotherhood/Thieves Guild mechanism. Far Cry 5 also warns you if you kill captives/innocents, but there is no penalty. Essentially, the only game that rewards you for being stealthy and choosing not to kill anyone is Dishonored. The low chaos ending is much more rewarding than the opposite.
Dishonored. That's the game I was trying to remember. I never did finish that game for one reason or another, though, I did like it. Being that stealthy is so nerve wracking to me. If your timing is off by a little, you are spotted and have to try and escape to hide again or you have to subdue at least one guard to get hidden again somewhere else.
I suppose one could sneak the whole way through most of Beth's games. For some reason, I liked being stealthy in Oblivion better than in Skyrim. Wouldn't it be cool if the game gave you an option if caught to try and fib your way out of trouble based on your speech skill? That one guard spots you as they come around a corner. Instead of just automatically attacking you, he decides to interrogate you instead....."You there! What in the blazes are you doing sneaking around back here?!" Okay, let's add the bonus for high charisma and luck here and roll......"So sorry old boy! I seemed to have dropped my coin purse passing by here earlier today. Would you help me look for it?"- and pass. Another way I looked for to deal with multiple "enemies" was a sleep spell or a gas or something. No need to send them to their maker this time around. Of course you could just charm lower level npcs into letting you go about your business. But, the illusion spells only work on characters up to a certain level- which is why I stopped relying on them at one point in the games. Will have to make or look for a mod that improves them.
As far as consequences go, I was thinking that the player could run into the deceased's children living in the street or by the road somewhere, poor and destitute because their mother or father had been their only provider. Do you take responsibility for putting them in that situation by giving them some money and helping them? Would you adopt them as your own? Would you laugh at their misfortune or ignore it? Would seeing the consequences of your actions make you think twice before killing again?
Let's say you killed someones brother and there were witnesses that saw you do it. Okay, you get a bounty and either bribe someone, pay the fine, or do some time in jail. But, what if some or all of that dead person's family wants revenge against you? What if instead of them being idiots about it and attack you in the streets, they secretly plot your demise. Let's say they are clever about it and try to use an opportune moment to strike- like when you're sleeping or something. Things could get very interesting... 