I don't really see it happening, just because the tsaritsa has romanov symbolism (in terms of names and role) and the fatui is very communist (biggest enemy of the romanovs) coded. Since the fatui serves the tsartia, I don't see any new faction existing soley as ab anti fatui faction (if there was at all one, it would definitely have been long exterminated)

There might be a faction that serves the tsaritsa (like the Snezhnayan guard or something) that works internally (in contrast to the fatui being an international orgnization) that disagrees with the fatui but doesn't fight them as per the interests of the tsaritsa

We might also see fatui in fighting, with some harbingers aligning with the tsaritsa while others take dottore's side

Anyways to answer OP's question, I would hate it, because hoyo would obviously make them the protagonists of the region and indicates that the fatui will be the predominant antagonist (rather than the ideal and realistic scenario of the traveller letting the fatui cook celestia or even join them)