He may not have had much choice, as the South was threatening mass civil disobedience.
They were in quasi-open rebellion. The war was not even a decade past. Squash them.
I get why Johnson was picked. It made sense given the state of the war. But while he would have been ok as vice president, once he inherited the role he was dead set on getting the South back in as soon as possible.
Not gonna be swayed on this, botching Reconstruction damaged the country in ways we are still dealing with.