I've been thinking a lot about immunity and trollification...
Interesting thoughts. 1% of immunity seems a good estimate.
However, the reasons for the death of so many immune population can also take in account a) Violence between humans, as society collapsed and people began fighting for what's left, and b) Beasts, because there's a very huge number of mammals out there, so it's not only 70 million trolls (aprox. 1% of the World's human population) but many more beasts. Just the number of cows is estimated on 1,5 billion, so it would be 15 million (large) cow-beasts to fight... Now add sheep, pigs, dogs, rabbits, horses and so many wild animals...
On my side, for some reason that I can't recall (had I read it on some comment?) I always assumed a 3% trollification rate.
Anyway I always assumed, as you said, that trolls are "half-immune" people. They didn't die from the infection because they had some resistance, but it was just enough to allow the mutations to take hold, not to overcome the virus (assuming it's a virus).
That would mean your idea of immune people having to fight their close relatives applies, whichever trollification rate existed. And yes, that's one good starting point for a story!
That it raises the trollifying probability of non-immunes is one quite interesting conclusion of that line of thought. Another fine idea for a story, and one that fits with what happened to Tuuri.
The eugenics part raises two questions:
First, we saw no evidence of that on the source material. But Minna may have not give much thought to the topic, or maybe we just didn't see enough to notice.
Second, there's the disadvantage of reducing the reproduction rate and the gene pool, which is worrying when you have a very reduced population. (not to mention the societal stress connected to the implementation of that ban...)
So any sufficiently protected community would, I believe, allow the reproduction of non-immunes, considering they should be kept behind fences and any outbreak immediately dealt. That, again, matches with the Hotakainens story.
But maybe some places see it on a different way? The non-immune couple that is banned from having kids and decides to move away to the wild, or to search for another community, so they can realize their dream looks like a good starting point for a story...