I don't feel like there's an unequivocal yes or no answer to this because it's so dependent upon the variables. If a person has been diagnosed with an immensely contagious and deadly disease like ebola, or there's a strong probability that he / she has been exposed to it, then I think you have to consider not just that person's rights but the rights of everyone else in society. We're all interconnected. A virus can be like an invisible, soundless viral bomb strapped to the person. On the other hand, I think there needs to be fair consideration for the impact a quarantine has on the individual and his or her family.
I live in Los Angeles where we've been affected this year by the measles and in the recent past by pertussis outbreaks. My boyfriend's former baseball coach had the measles, but the majority of others I personally know who were either diagnosed with it or exposed to it and are unvaccinated or immunocompromised are minors. The Health Department gave them and their parents detailed instructions on how to self-quarantine but is not militant. There wasn't a police car sitting outside their door waiting to arrest them if they dared to go outside. It is a misdemeanor here to violate quarantine orders, though. The ones who most stringently enforce their isolation protocols are schools, dance studios, equestrian centers, and the like where kids who were / are under quarantine are not permitted to be in attendance. There's a magnet school for the performing arts that is on the campus of Huntington Beach High School, and many of my friends from dance go there, few were impacted by the school board-mandated quarantine that was issued for all those who are unvaccinated or immunocompromised after a sophomore was diagnosed with the measles in January. For the three week infectious period the students could not be on campus for school, athletic practices, club meetings, or anything else, and also were prohibited from attending any off-campus events and activities. A dance studio had initially been reluctant to take firm action but finally did after a student there was diagnosed with the measles. All kids who were unvaccinated or immunocompromised were asked to refrain from attending the studio. They were reliant upon parents' cooperation since they did not know the vaccination status of each dancer.
Parents can obtain personal belief and religious exemptions from the required immunizations, but most schools stipulate that they will agree to quarantine their child if there is an outbreak. I have no idea how it works with public schools but the private schools I've attended require parents to submit a contract to reenroll their child for the next school year, and by doing so agree again to adhere to policies. There's a medical database and parents have to keep it current for us. We have a specific protocol in place for contagious illnesses. The thing that sucks is that most of the ones I know who've been impacted are teens who have developed belief systems of their own but are subjected to the quarantine and bans either because of decisions their parents made on their behalf to not vaccinate them, or because of a compromised immune system. They are not culpable for the choices that put them in that predicament. But nevertheless I think the quarantines are fair and reasonable, because the majority of the time (with unvaccinated kids) parents have consented to being in compliance with them even if the kids themselves have not given such consent. They protect both the school community and society at large, and have been effective at helping to minimize the destruction of the outbreaks. This was also the case with the whopping cough outbreaks that hit private school junior high students here back in 2011 and 2012. Most schools here use online education software platforms like Haiku Learning that enable students to virtually attend classes from home. At my school they set up a camera to record the class and then put the video online, and you can IM / email the teacher and others in your class. It's works pretty much like the actual online school where I take classes, except the classes aren't streamed live. It's not like quarantined kids are just completely missing out on their classes for that whole duration. I have no idea how it works for adults who are barred from their workplace and if they can telecommute.
The college I'll be attending in the fall has a far more rigorous process for being granted exemption from the vaccination requirements. Students who receive the exemption consent to a voluntary quarantine in the event of an outbreak. Again that's totally reasonable to me.
As for the government itself imposing a quarantine I think it's morally fair but the way it's managed should be sensible and proportional. Strong-armed action should only be taken if the person is willfully showing disregard for the quarantine and wantonly putting others in genuine imminent risk. The nurse who defied the ebola quarantine she was placed under by going for a bike ride on an empty street in a rural area wasn't posing the same level of risk as she would have been if she'd be at Grand Central Station during rush hour, or if she was actually symptomatic. I 100% support the hospitalized quarantine of people who have been diagnosed with ebola. If a person with a less serious but still potentially lethal disease like measles had been in adamant refusal to cooperate with self-regulated quarantine protocols, then forcing them into a hospitalized quarantine could be the morally responsible action. Again, I think the person should be in direct disregard of orders and posing a genuine threat before such an action for a lesser disease would be justifiable. An individual has liberties but they are not without limitations and have to be in compatibility with the liberties of others within the society.