I might have more on this later but I thought I would bring a little history into recent declarations of who is in change when it comes to quarantines.
The 1824 Gibbons v. Ogden Supreme Court case clearly states that the State governments are in complete control of quarantines in their own states. This was a commerce case and Marshall stated the President has the power to quarantine anyone coming into the nation and in interstate travel, but only governors control quarantines within their own state.
Historically Speaking 