Something funny is going on with people's moral reasoning here and I suspect it isn't peculiar to rationalists, but reflective of something in wider culture.

Maybe it is peculiar to rationalists, or I should say, "rationalists": people who think they're rationalists. Quarantining people with colds and not quarantining people returning from places with Ebola have this in common: it is the opposite of the practice seen in the wider world. Therefore, if you take this view, and assemble clever arguments for it, you must be being more rational.