Actually going extinct would seem to be a bad thing, but a close call can, in principle, be a good thing.
Pathogens can be a heavy burden on a species, worse than a 50-lb sack of cement. Lifting that burden can have a big effect: we know that many species flourish madly once they escape their typical parasites. That’s often the case with invasive species. It’s also a major strategy in agriculture: crops often do best in a country far away from their place of origin – where the climate is familiar, but most parasites have been left behind. For example, rubber trees originated in South America, but they’re a lot easier to grow in Liberia or Malaysia.
Consider a situation with a really burdensome pathogen – one that specializes in and depends on a single host species. That pathogen has to find new host individuals every so often in order to survive, and in order for that to happen, the host population has to exceed a certain number, usually called the critical community size. That size depends on the parasite’s persistence and mode of propagation: it can vary over a huge range. CCS is something like a quarter of a million for measles, ~300 for chickenpox, surely smaller than that for Epstein-Barr.
A brush with extinction- say from an asteroid strike – might well take a species below the CCS for a number of its pathogens. If those pathogens were limited to that species, they’d go extinct: no more burden. That alone might be enough to generate a rapid recovery from the population bottleneck. Or a single, highly virulent pathogen might cause a population crash that resulted in the extinction of several of that species’s major pathogens – quite possibly including the virulent pathogen itself. It’s a bottleneck in time, rather than one in space as you often see in colonization.
Such positive effects could last a long time – things need not go back to the old normal. The flea-unbitten species might be able to survive and prosper in ecological niches that it couldn’t before. You might see a range expansion. New evolutionary paths could open up. That brush with extinction could be the making of them.
When you add it all up, you begin to wonder if a population crash isn’t just what the doctor ordered. Sure, it wouldn’t be fun to be one of the billions of casualties, but just think how much better off the billions living after the bottleneck will be. Don’t be selfish.