Since you don't seem very familiar with Johnson's term in office, here:
http://www.sewanee.edu/faculty/Willis/Civil_War/documents/AndrewJ.html
Those who were exempted from this amnesty had to appeal directly to Johnson himself. Within months Johnson had handed out thousands of pardons.
Now, I'll ask again...do you have any evidence to back up your claims? Or are you simply making brash assumptions?