A note regarding the real world: If emission theory could be disproved by the experience of lightless rooms, it wouldn’t have been espoused by many of the brightest minds of an epoch. In general, I’d be careful about slipping into any history of ideas that implies pre-scientific thinkers were idiots. 
Emission theory was an application of the broader epistemological principle of “like is known by like,” which wasn’t nonsense (though also not as broadly true in our world as many premodern thinkers believed). If the minute amounts of light emitted by the eyes did not encounter the light emitted by more significant sources like fires or the sun, there would be nothing to “know”/see. A dark room, on this theory, was missing one of the necessary components for sight.
To return to the gameworld, a Theurge in trance in a completely dark room would “see” light emerging from other people’s eyes. Perhaps that means that physics in the gameworld really is Aristotelian, or perhaps Telos-vision is interpretation as much as perception, strongly influenced by what you believe/expect to see.
This will definitely be an option. Of course, if you don’t bring the helots into your army, you’re inviting other rebels to bring them into theirs.
There is in practice a fuzzy line between the noble and merchant classes, as desperate nobles lose their land and resort to trade, while the most successful merchants marry into lower noble Houses. But the great majority of nobles are not merchants, and vice versa.
Rejecting Theurgy and starting an anti-Theurgic inquisition will be a chooseable path. I can’t imagine it will lead to you being one of the major contending factions in Book 5 – unlike an inquisition with Theurgy – but you could end up as a faction based out of a patch of Shayard, and either come to some accommodation with the other Theurgy-using factions or live as a perpetual rebel and foe to them.
I’m traveling away from my notes – will check when I get back.
Let me qualify that statement. If you want to be the leader of one of the major continent-spanning factions by Game 5, on a par with the biggest internal and external actors, you need to have Theurges. But that’s not going to be the only way to “win”.
You may choose to be one of the smaller factions, and consider victory to be surviving and establishing stable relations of one kind or another with the other successor states. You may choose to not consolidate your rebellion in any one bit of territory, but remain a permanent rebel challenging the status quo, either violently or non-violently.
I’ve realized that the “choice of rebels” shouldn’t be limited to creating a new empire or major nation, with all the compromises that that would inevitably entail. A purist rebel will have other choices.