Paranoid Productions' The Church in the Darkness is a stealth infiltration game with a side of mystery and human psychology. But it absolutely does not endorse the thought of joining a cult.
Loosely based on several different and problematic cults, though the easiest touchstone is of course The People's Temple (better known as "Jonestown), the game is not based on any one cult. There are aspects of the Branch Dividian cult from Waco, TX and the Heaven's Gate group from San Diego, CA.
That said, the game is pretty anti-cult, which is a rather uncontroversial choice. However, depending on the randomly generated personalities of the cult leaders and cultists, you may come across a more peaceful cult than most.
The official game description will give you more information:
No one is forced to join a cult. It welcomes you. It understands you. It envelops you until the words become more than truth – they make you whole. In the late 1970s, the charismatic Isaac and Rebecca Walker lead the Collective Justice Mission. Labeled radicals and feeling persecuted by the US government, they relocate their followers to the one place they believe they can create a socialist utopia: the jungles of South America. There they build Freedom Town. But relatives left behind in the US become worried: what exactly is going on at this compound in the jungle? The Church in the Darkness combines unique narrative with tight top-down action-infiltration gameplay in an open-ended environment. As Vic, an ex-law enforcement officer, you travel to South America to get into Freedom Town and check on your nephew, Alex. Play how you want – you can avoid detection completely, take on the guards using non-lethal methods, or kill anyone who gets in your way. But you'll have to live with the consequences of those choices. Every playthrough offers unique gameplay scenarios and story elements, with different character personalities and a shifting narrative told through investigation and action. You soak up the story through the town PA system, where the preachers share their dogma and beliefs. You find documents and letters scattered around camp which clue you into the true nature of Freedom Town. How dangerous are the Walkers? Who are your allies and enemies? How far will you go to uncover the truth and save these people?
The game play is all stealth, exploration, and investigation. Players will need to sneak around the cult grounds to try and rescue their sibling, but they can also affect the trajectory of thr cult itself and lead a coup. If they get the right information and talk to the right people.
You do get bonuses for playing non-lethally, and your actions will affect the NPCs and how they interact with you.
Between the randomly generated personalities of the cultists, randomized locations of objects and NPCs, and lethal vs non-lethal options, The Church in the Darkness is highly replay-able.
You can see a bit of the game in action below.