Ultimately that is the nutshell. The ability of the government to freeze individual (or even masses of people) in the spirit of safety is the twin-edge sword that allows the government to suppress freedom.
The ultimate solution (in both cases), in my opinion is to be avoided. Allowing infectious people to travel threatens the lives of the general populous. Allowing government to lock up scores of people on a trumped up issue threatens our very liberty.
Lucky for us - we have the Bush/Hillary test. Pick the one you hate and ask yourself that if the President didn't lock up individual with an infectious disease (oh, for example, the plague) - what would you think.
Likewise, ask yourself what you would think if the President if they started locking people up claiming it was for our own safety.
(I note with humor that if Clinton had considered locking people up... what certain individuals -- who don't have a clue about whats at stake -- would've said.)