My guess was that Ensi may have been doing the masks and quarantine thing because everyone had to? For all they knew, there might have been variants of the rash that could affect the previously immune? One of the fan writers, I think Seilann, played with that idea in a story called ‘Burning’, a few years back. It’s on Archive. And real-world diseases do that. Consider the variant strain of Covid that has turned up recently in the UK.
Certainly, there can have been any number of
reasons back then - except one: Ensi had already started to train Lalli instead of Onni, so they already
knew about immunity (because it is established that Onnis lack thereof was the reason why Ensi switched padawans).
Doesn't change a iota about the fact that the flashback doesn't offer us a
reliable indication of who exactly has been immune or not - beyond "it is already known" (Ensi and Lalli), "...
not" (Onni, Tuuri, and the entire rest of the family, per Tuuri's statement to Emil), "looks like she wasn't" (Hilja), "
sounds like he wasn't" (Tapsa), and "
few were" (Tuuri's statement, as well as the final death toll), though.