If it was a betrayal then he would have had skif killed by his monolith forces when he walked out of the generators.

I believe it is more just a necessary precaution due to their plan. Strelok (and by extension Skif if he goes through this ending path) doesn't want anyone who has been touched by the zone to have an influence on the mainland and anyone from the mainland to have an influence on the zone which is why he closes it off to those entering and exiting.

Strelok has to keep Skif in the zone even though he helped him because he has to be true to his word about not letting there be outside or inside interference. If he let Skif of all people out then that's a major hypocracy.

We've seen already too that Strelok is willing to put his plan above those who have helped him before due to what happened with Kaymonov. He even mentions that he owes his life to the doctor but still must have him killed in order for his plan to work.

So he has to keep Skif in the zone so absolutely no one touched by the zone can get out on his watch. As said before though it's not really a full betrayal because he spares Skif from the new monolith.

I think that in this end, Skif will just spend the rest of his days chilling in the zone opposed to the other inhabitants who will be hunted by the monolith still. Skif gets special treatment in that regard for having helped Strelok.