I think we can refine this somewhat.
For comparison, the Thirteenth Amendment, and especially the Fourteenth and Fifteenth, were passed by means that were arguably extra-constitutional. The Thirteenth was passed while the Confederate states had excluded themselves from the ratification process by rebellion (though one could argue that applying the amendment to those states after they were reabsorbed into the Union was little different from applying extant amendments to newly incorporated territories). The Fourteenth and Fifteenth were passed while large segments of the population of former Confederate states had been temporarily excluded from voting by congressional fiat. Without those measures, these amendments would never have been ratified, but it's hard to object to those measures because the amendments made for a far more equitable legal system. The Thirteenth abolished slavery, the Fifteenth guaranteed voting rights to former slaves, and the Fourteenth — the most significant amendment ever passed — gave citizenship to everyone born on US soil, gave "equal protection of the laws" to everyone within US jurisdiction, and applied the protections in the Bill of Rights to state governments as well as the federal government. These amendments are as much a part of the bedrock of our legal system as the Bill of Rights itself, and they represented a massive increase in freedom for the people of the United States in general, not just former slaves. Their validity has never, as far as I am aware, been legally challenged, and while the white backlash to Reconstruction rendered them toothless in the late 19th century, they remained on the books and were finally fulfilled with the civil rights acts of the 1960s.
So to a certain extent, the ends can justify the means. A large segment of the white population of the South had to be temporarily deprived of their voting rights so that the rights of all Americans could be expanded permanently. The question is: what measures can we take to fix this problem that will stick over the long run?