Sadly with reduced populations there's always a high risk that what population you have left ends up with gaps in its immune system. If you then breed from those reduced stocks you end up with a population that might have healthier numbers, but which has no resistance or reduced resistance to strains which, in previous generations when the population was more extensive and varied; would only have harmed local popualations not the "national" population.
Hopefully the populations we have can be protected from this; or at least managed to mitigate the risk. The real issue though is still the same; vast habitat loss combined with invasive species out-competing them.
As always with the reds the question comes back to the matter of what to do with the greys. Not to suggest that removal of the greys is all that is needed; but that without that step nearly any other plan is destined to fail.
I've read that there is some interest in pinemartins being reintroduced to areas of the UK and that they predate more on greys than reds; apparently due to the heavier build of the greys which means they can't retreat to the farthest edges of the branches and thus the pinemartins can get them. Whilst the reds are lighter and thus able to go further and out of the reach of the pinemartins.
Of course pinemartins have their own problems including generations of persecution by farmers and gamekeepers. With pheasant shoots being as popular and profitable as they are and already causing strife with wild raptor reintroductions one must wonder what chance the pinemartin has at making a meaningful re-establishment in the mainland UK. Of course if that is true then we when we come back to the squirrels we still have to do something about the greys.