I am currently studying the Reconstruction period and really struggling to get my head around some of the chronology and different policies. I know it made a lot of news when Mississippi finally ratified the 13th Amendment abolishing slavery last year. I thought that one of President Johnson's prerequisites for readmission into the Union, even before the onset of Radical Reconstruction, was that the states had to accept the end of slavery. So how was Mississippi readmitted into the Union when it refused to ratify the 13th Amendment?
This is sort of a legal question / legal history question.
First of all, for a constitutional amendment to apply in a state, the state need not ratify the amendment so long as the other prerequisites for the amendment are met. Thus, slavery has been unconstitutional in Mississippi under the U.S. Constitution for over a 100 years.
Second, former confederate states were just required to abolish slavery, not ratify the Thirteenth Amendment. After the Amendment meets its prerequisites to get into the Constitution, ratification is just a formality. Mississippi amended its state constitution to include a prohibition on slavery shortly after the civil war. See http://law.justia.com/constitution/mississippi.
Hope that helps.