Dickens (a tale of two city, chapter 1): what do "they were awake" and "was to be atheistical and traitorous" refer to?

Solution 1:

I think that all "they" or "them" in the context are the Woodman and the Farmer. The last sentence can be paraphrased as "those who notice that they(the Woodman and the Farmer) are awake(working) are regarded atheists and traitors." Because the Woodman and the Farmer are working for revolution.

Solution 2:

For purposes of understanding this sentence, it's important to bear in mind that (as Dickens notes earlier in the same paragraph) the Woodman is Fate and the Farmer is Death.

In 1775, when the metaphorical scene with the Woodman and the Farmer takes place, France was still firmly under the control of the king and his agents in government. Therefore, for any French citizen to have suggested in 1775 that the Woodman (Fate) was awake and preparing the guillotine for work against the upper classes of the country or to have suggested that the Farmer (Death) was awake and had already selected the farm carts that would later be used as tumbrils to transport the doomed victims of the coming Terror to the place of execution would indeed have been viewed as traitorous (insofar as it stirred up popular discontent with the existing regime) and, arguably, atheistical (insofar as it denied that God approved of the existing social order and of the king as his chosen political instrument).

In any event, purely as a matter of identifying the referents that the OP asks about, (1) Fate and Death were awake (and about to become active) after centuries of somnolent acceptance of the existing monarchy, and (2) an ordinary French citizen who suspected that Fate and Death were awake would on those grounds have been deemed atheistical and traitorous, Dickens says.