You, sir, are not intellectually honest, and here’s why:
John Jay first expresses a general concern about foreigners in the administration of the government, which is immediately followed (in the same sentence!) by the words “and to declare expressly that the command in chief of the American army shall not be given to, nor devolve on any but a natural born citizen.” The construction allows of no other intellectually honest interpretation but that Jay was asserting that the explicit requirement that the President be a natural born citizen was the foremost measure that should be taken to prevent foreigners playing any managerial, ministerial or executive role in the administration of the national government.
You are correct - Jay was asserting that the "natural born citizen" requirement was the foremost measure that should be taken to prevent foreigners playing a managerial, ministerial, or executive role in the administration of the national government. As I read it, the concern about foreigners led Jay to suggest the "natural born citizen" requirement, as a means of preventing a foreigner from immigrating to the U.S., becoming naturalized, and running for President.
We may disagree about whether a person born in the United States to foreign parents (or, to one U.S. parent and one foreign parent), is a "natural born citizen," but it is quite a stretch to say that such a person is a foreigner. If Jay was concerned about foreigners playing a managerial or executive role in the national government, then prohibiting the U.S.-born child of foreign parents (or, again, one foreign parent and one U.S. parent) seems to be a bit beyond the scope of his concern.