The courts have also consistently rejected overly clever de facto travel bans via regulatory mechanisms intended to prohibit the use of common modes of transportation. Courts have taken a very dim view of arguments, which the government has made in the past, that e.g. free travel can effectively be restricted to walking. American courts have ruled in the past that the right to travel extends to the use of common modes of transportation.
If fundamental Constitutional rights could be suspended every time the government claimed an emergency, Americans would have no rights in practice. There is no allowance for the blanket suspension of fundamental rights by reason of public emergency in the US.
https://www.usatoday.com/story/travel/airline-news/2020/03/1...
That is a very different legal authority than de facto blanket bans on free movement of Americans, which is expressly disallowed by the Constitution. This has actually been adjudicated several times in the Supreme Court, which has consistently rejected attempts by the government to use regulatory technicalities to deprive people of their right of free movement via common modes of transportation even subject to due process.
This is not new territory, there is extensive court precedent surrounding the right of free travel in the US. It is on the same tier of right as freedom of speech in the US.
In other words, "you might have COVID-19" has the same authority granting power as "you might be a terrorist" or "you might be a child pornographer", which is to say, very little absent specific evidence.
Also, I think you drastically underestimate what can be legally done under the aegis of "you might be (insert undesirable class here)".