The question at hand is whether or not the government was abusive of its tarrif power. A quick look at the Constitution might help:
The Congress shall have power to lay and collect taxes, duties, imposts and excises, to pay the debts and provide for the common defense and general welfare of the United States; but all duties, imposts and excises shall be uniform throughout the United States;
Does protectionism fit into one of those categories?
The Constitution does not say that the tariffs cannot be protectionist in nature, nor does it define what protectionist is. All it says is that it must be applied uniformly throughout the country.
And on the subject of protectionism, the Morill Tariff as passed also placed significant duties on molasses, raw cotton, sugar, tobacco and tobacco products, and naval stores. All items that the south produced in quantity. Did not the Morill tariff provide a protectionist safety net to the south as well?