I think all the three options are pretty viable. I doubt our rebels will just forget about all those weeks when they were properly fed and armed the moment they are back among the Helot camps. Nor will they forget about the Eclect/Kenon/voices in their heads, which is a massive hit to the legitimacy of the oppressors. Nor do I think the Kryptasts will have an easy time trying to track down pairs of Helots, it will just be too much of a hassle and by the time the Helots have heard the news it will already be too late.
Trying to openly fight the Hegemony like an army is obviously suicide, but it still seems viable to pick our battles and destroy garrisons, weaker forces, defend our forest, and so on. The Theurges are expensive, and as the demand for blood increases, so will the brutality of the Hegemony. One day they will have to cross some lines and then people will rise up, just like we saw in the fourth Harrowing.
And then you can just try to just hide in the woods and survive, growing in numbers and strength, and hope that something happens one day that will allow your rebellion to explode in size. I like burning temples and smuggling dye just as much as the next guy, but this seems like the safe but unambitious choice.
Also, I am pretty sure that the Kryptast threat is exaggerated. The Hegemony just wants us to think that they are all-powerful and all-knowing, to scare us into submission or caution. If we were really infiltrated by any proper Kryptasts, we should have died a long time ago.