If the government relinquished its role in handling contagious diseases, the public would be far safer.
First and most obvious: the government restricts freedom of association, and more specifically, the freedom of property owners to exclude whomever they desire. In the current legal environment, it would be pointless for airlines, bus carriers, amusement parks, hotels, etc. to maintain their own list(s) of people with contagious diseases. If these people weren't considered health risks by the government, then they could sue if (say) Disneyworld refused to let them into the park.
But suppose the government did act as if owners really had the right to control who used their property. What voluntary institutions would spring up to help a free society cope with the problem of contagious diseases?
There are two competing principles that we need to consider. On the one hand, it's bad for business to exclude potential customers for health concerns, especially if it turns out that the exclusion was based on mistaken information. On the other hand, it's really really bad for business if a bunch of customers contract a contagious disease from another customer because of lax oversight.
Since business owners are in no position to make these judgment calls themselves, they would gladly pay for independent health experts to advise them on how best to run their operations and minimize the risks to their employees and customers. [comment: isn't the tax-subsided CDC suppose to be providing that information now?] Through such consultations and (as always) the profit and loss system, over time an efficient portion of resources would be channeled into disease prevention. For example, salad bars would have sneeze guards, critical employees would wear gloves, and bathrooms would have soap dispensers.
But beyond these fairly obvious safeguards, more sophisticated ones could emerge. For example, specialized consulting firms could assemble teams of medical experts to monitor the world, and identify individuals for the airlines who are at risk for contagious diseases. In order for these flagged travelers to buy tickets and board the plane, they would first need to be checked by the medical consultants (or by their own physicians, if the airlines recognized their competence).
The great difference between voluntary mechanisms versus the monopoly CDC is that the former would have every incentive to do a good job. If an airline turned away certain customers because Ace Medical Consultants said they had TB, when in fact they didn't, this would be horrible for business. Ace's competitors (who had a better track record) would advertise this fact in their brochures and the airline would switch if it thought the rival could do a better job.