What could be Johnson's reasoning for not further punishing Confederate leaders?

Johnson's reasons for not punishing Confederate leaders was that he wanted to reunite the nation as soon as possible. At first, he followed a harsh system toward the frustrated Southerners. The southerners were denied political freedoms in the military or governmental role since they supported the Confederacy during the American rebellion.

On May 29 the year 1865, President Andrew Johnson issued his Proclamation of Amnesty and Reconstruction, which laid out provisions for governing the restoration of citizenship and rights to former rebels. Johnson announced a pardon to all former Confederates only if they agreed to support the Union and obey laws against slavery. He also allowed former officials of the Confederacy to run for office in their states new elections.