Prior to that there hadn't been a rebellion. Legislation was passed to combat the rebellion. The matter was taken to court and the court ruled that the Constitution hadn't been violated. That's the way it works, regardless of the date of the ruling.
From the decision, "[t]he question, therefore, is, whether the action of Congress was a legitimate exercise of the war power." Was it a war? When did Congress declare it to be a war? Or was it a rebellion? In 1866 SCOTUS determined 9-0 that the Constitution applied to all men at all times, that it could not be suspended by a war. Only a moron can take '[n]o person shall be ... deprived of life, liberty, or property, without due process of law; nor shall private property be taken for public use, without just compensation', and make it mean something else.