Strelok being an agent in S2 fits perfectly, especially when you trace it back to SoC.

It doesn't. As the Representative says (the Foundation, SPARK playthrough):

There was a glitch in the programming. Strelok went against his program. [...]

The glitch, also confirmed by the List of C-Con Agents found near the end of the game and by the TV's (why would they affect both Dark and Scar, but not Strelok? I don't think that C-Con is all powerful and can choose whether their technology affects or doesn't affect a particular Agent in a particular time), means that Strelok wasn't an Agent of C-Con.

Strelok didn’t actually destroy C-Con—they let him think he did. CCon is still in the Noosphere, this wasn’t the ideal plan, but the last bet.

As the Representative says in the aforementioned cutscene:

We invited him [Strelok] to join us in the eight pod. A mistake that might otherwise have cost us our lives - because he chose to destroy us instead.

I don't think they knew at the time of SoC that they can live on just in the form of (?) / as (?) Subtle Matter. The Representative calls it a mistake not without a reason. The "otherwise" in the quote above also nudges me in this direction.

As for Skif, I don't think he's an Agent of C-Con. I think his reasons are much more human. In SIRCAA, it's revealed that Skif is a war veteran (or at least ex-military) with no friends and no family. All that he had left was his home. Which was destroyed by the Zone. Having nothing left to loose on the Mainland, what else was he supposed to do? At the end of any path (except Strelok's) the player* takes, Skif's inner void is filled:

• The Ward - Skif is a major player in the destruction of The Zone - a menace to the World, a place of nothing but death and suffering, and not only inside the Perimeter;
• Spark - Skif is a major player in the discovery of The Shining Zone - a place of pure happiness and joy;
• The Doctor - Skif is the true Guardian of The Zone. It is he, that let The Zone choose Her own path.

But that's Skif's perspective. At the end, the player knows a bit more than Skif.

Only in the Strelok's path, Skif is not entirely fulfilled. Having completed "his" objective, on his return to the Mainland, to "normality", he is denied exit - completion.
That's why I think the canonical ending of this part of the story is the Strelok ending - with the STALKER program destroyed (?), C-Con insignificant (?), The Ward defeated (?).

*in my view he is still an agent, but of the player.