Let's constitutionally analyze this: Who Is in Charge: The federal government

Acts to prevent the entry of communicable diseases into the United States. Quarantine and isolation may be used at U.S. ports of entry. OF COURSE, THE FEDERAL GOVERNMENT IS SUPPOSED TO REGULATE THE BORDER.

Is authorized to take measures to prevent the spread of communicable diseases between states.

OF COURSE, THE FEDERAL GOVERNMENT HAS THE POWER TO OVERSEE INTERSTATE COMMERCE AND OTHER INTERSTATE MATTERS.

May accept state and local assistance in enforcing federal quarantine.  OFFERS of HELP ARE NOT FORCE
May assist state and local authorities in preventing the spread of communicable diseases.

Nothing mentioned above describes a general jurisdiction for the federal government and its agents to do what they want within a state of the Union. The borders, the lines between the states, and the federal territories are under federal jurisdiction.

Sorry, can't format what I am writing :)