First off, on spoiler policy: the only thing really spoiler protected on this forum thread so far has been the loredump I gave on the details of how Theurgy works. It’s been hard to sustain that–and I don’t fancy policing the thread to keep other future ideas and details spoiler protected.
Once I’ve posted Ch 1, all those Theurgy details will be common knowledge; following that, I don’t intend to share any more huge spoilers on the thread, just the broad framework and a few hints about future games. I don’t think we’ll need spoiler protection for that.
I’d like to be a little more discriminating on the wiki, which may attract more casual fans. If you’re adding material to the wiki, if it doesn’t come from the game, drop it in spoilers. I’ll move it over to the regular game lore section if I think it’s just interesting world detail rather than something likely to spoil someone’s enjoyment of a future game.
Religion is a famously odd category, with blurry and contested boundaries. It’s true that in the XoRverse, it would be basically impossible to deny the reality of teloi or the power than comes from reflecting on them; to that extent every Theurge is “religious.” But that doesn’t mean they need to think there’s a God, even an Unmoved Mover one like Xthonos, let alone that the Canon (or any other religion on offer) is the best articulation of reality.
Materialism has its teleologies too. Skeptics can believe that the fact that things have purpose (to fall, to rise, to cut, etc.) is a brute fact of the universe, not the result of any Supreme Being’s intention.
The stories about Angels in the Codex certainly have them presenting themselves in physical form to their Eclect. It’s an exceptional event even in the stories, though. Much as in our own world, the vast majority of believers get by without any flashy personal epiphanies. And I can confirm that the Rebels saga will never feature an unambiguous intervention by the Angels, the Forgotten Gods, Ummay and Kormuz, or the Theoi – no parting of the Red Sea, no Athena sending fog to protect Odysseus and then appearing to him for a chat. Does that mean the gameworld is one without gods? That’ll be up to the reader to judge, similarly to everyone in our world who lives without personally witnessing a “visible real effect.”
A plausible alternative explanation, as I said on those old threads. 
There is a tension here, if not a necessary trade-off. Religion (as the most widely proposed etymology implies) binds people together. Even in our own prosperous, relatively stable Western hegemony, it can’t be treated solely in terms of individualistic “spirituality.” In a centuries-old empire collapsing into chaos, you’re going to want some social binding factor if you’re going to establish any sort of new order.
But almost anything that binds people together also divides them from outsiders – even, as real-world history bears witness, philosophies that have love, compassion, tolerance, etc. at their heart. Keeping your compassion-religion or tolerance-religion (let alone justice-religion) from being a barrier to a shared life with those who believe differently is a full-time job.
A skeptic needn’t abandon the socially integrating function of religion; as you’ve noted, there are “religions of non-religion” that bind people together strongly, and Kenonism may become one of those. But the more you want to bind people together, the more you’re likely to alienate those outside.
Rape should be a Harrowable crime, and a lower-class person found to have raped a helot would be Harrowed. The consequences of a rape allegation by a helot against a noble would be punishment of the lying accuser.
Only the prestige that comes with a close family connection to a Theurge.
To protect the Theurgic secret, all children of Theurges are given up for adoption to aristocratic families and raised separately from their parents. Kleitos was the first Thaumatarch to declare that he would personally comply with this policy; though as far as anyone knows, he’s never had any children to give up.
In theory, Theurges select the helots for Harrowing by inspiration of the Angels, who don’t take appeals from aristos. The reality will be explored more in Game 2 Ch 2.
No. That’s something that Theurgy is very good at nipping in the bud, and human capital is too valuable to be wasted in that way.
As @Sneaks correctly assumes, if it were that easy, the Hegemony would have their Long War down south instead of Halassur.
Never. Completely unthinkable for them.
Yes. She was facing certain death at the Hegemony’s hands, and where others might have considered fleeing to the wilderness to join the bandits, that obviously wasn’t an option for her. In that extraordinary bind, she didn’t respond fatalistically or passively, but went for a slim chance of survival. That’s a reasonably rare choice in an established totalitarian state, even one approaching a crisis; it shouldn’t be all that surprising that the MC hasn’t previously met someone like that.