OK, firstly, before even acknowledging that these NPCs are sapient true-AI, there'd likely be a lot of complaints against players being able to cause so much abuse in a game.
Most games today don't include things like rape or torture except in very specific scripted instances, and then only in certain types of games. Many games allow killing of pretty much any other character in the game - but either don't include children or make children immortal. (For example, Elder Scrolls: Skyrim)
One of the reasons for this is that otherwise there would be public outrage - and this is with NPCs that have no memories or emotions, and can be reset just by reloading a save or starting a new game. NPCs showing an emotional reaction, and being able to remember the events, would increase this by a lot even if the NPC wasn't true AI.
Giving human rights to AIs would be hard - just because different countries would likely have different stances on it, even if it's not deliberate (for example, a country might just not get around to updating their laws to include AIs). As an MMORPG, you would have players throughout the world that would then be under different laws concerning treatment of the NPCs.
And even if the entire world does grant true AI human rights, the process would take years and your company might not survive that long.
A better thing to do is include the safeguards you should have had right from the start. And if you make some changes now, you hopefully won't get in trouble when AIs are given human rights.
This is a game, and thus there are some things that are very different from the real world. It also means that we get to mess with the laws of physics as much as we want, since the only physical laws that exist in the game world are the ones we create. We can even retroactively change how physics works based on the actions of characters.
Firstly, players raping others. Player characters, unlike AIs, don't need to reproduce. Just prevent them from doing anything related to it.
Secondly, when player characters die, they probably respawn. This is true of pretty much all MMORPGs and likely is the same for your game. To keep things fairer, let your NPCs respawn from any death other than old age.
Thirdly, many MMORPGs have safe non-combat areas - even if it's otherwise a full PvP game. In these areas, prevent crimes from being committed, including killing, stealing, and holding a character against their will. It may be a good idea to do this for every NPC town. Their surrounding farms, etc. can be outside safe areas if desired, but they will have a safe place to retreat to.
Fourthly, your NPCs likely have some kind of legal system to govern themselves. Help them out a bit by allowing many of these laws to also apply to player characters.
You also have far more power than any player or NPC, if a player gets too far out of hand you can ban their account. All MMORPGs are willing to ban player accounts (either temporarily or permanently) for things like harassment. You also have this power over NPCs, but from your description it seems like they aren't causing trouble. Also, if one does decide to become an evil overlord and declare war on the players, you could probably get people to let it slide by announcing it as a game event or something.
Finally, be prepared to watch how things progress. Take input from both your players and your NPCs. You won't be able to keep everyone happy, but you may be able to keep most of them happy.
Of course, all this does still leave open the question of: What happens if your company fails? Who pays to keep the servers running? If your NPCs are given human rights then turning off the game would be committing genocide. Cutting them off from the internet to prevent players logging in may be fine, but although network costs are high for MMORPG, you still have the rest of the server costs and maintenance...