Congress had the power to regulate the Territories. But not to exclude clauses of the BoR.
Congress, as in the previous sentence. The Congress of the Confederation had outlawed slavery in the Northwest Territory (which eventually became all or part of six states). This was in the Northwest Ordinance of 1787, which is pre-constitutional law. In fact, elements of that law are still in effect today, although those areas have long since ceased to be territories.
The Congress of the Confederation, containing in one body the legislative and executive functions in that form of government, established a legal precedent with that legislation, so far as organized territories were involved. One cannot correctly claim that the Northwest Ordinance was "unconstitutional," as it preceded that document. Nor can one claim that subsequent law, such as the Constitution and its amendments, were intended to overturn the precedent of congressional control of the territories. Indeed, many of the same people involved with the development of the Constitution in 1787, and the 1st Congress of the Constitutional Union in 1789, were involved in drafting and passing the Northwest Ordinance. It was a given that Congress had the power to regulate slavery in the territories, and no amendment proposed in the 1st Congress was intended to address that issue.
You are the one who seems to be on the horns of a dilemma.