The consitution specifically says that the President must enforce all laws and the Consitution. It is done through the "Take Care Clause".
This clause is meant to ensure that a law is faithfully executed by the president[40] even if he disagrees with the purpose of that law.[43] Addressing the North Carolina ratifying convention, William Maclaine declared that the Faithful Execution Clause was "one of the [Constitution's] best provisions."[41] If the president "takes care to see the laws faithfully executed, it will be more than is done in any government on the continent; for I will venture to say that our government, and those of the other states, are, with respect to the execution of the laws, in many respects mere ciphers."[41] President George Washington interpreted this clause as imposing on him a unique duty to ensure the execution of federal law. Discussing a tax rebellion, Washington observed, "it is my duty to see the Laws executed: to permit them to be trampled upon with impunity would be repugnant to [that duty.]"[4
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The Constitution says that:
Amendment I
Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof;
Therefore no governor can prohibit the free exercise thereof.
With these two clauses the President must enforce the Constitution and can override the governors.