Pardon = the defendant is forgiven his crime and released from prison, but the fact of being guilty of the crime remains, i.e., the defendant is forgiven for his bad acts.

Amnesty = the defendant is cleared of legal guilt for the crime and the fact of having committed the crime is also cleared, i.e., it is as if the defendant never committed a crime at all.

Pre-emptive amnesty is more simply referred to as "immunity."