Any otherwise legal act becomes a crime when done in an act of bribery, in obstruction of justice, or in the commission of other crimes.
For example, it is perfectly legal for you to drive a car. But if you knowingly drive a car transporting a bank robber away from his crime, you are guilty of a crime.
Libby's acceptance of the commutation was in furtherance of obstruction of justice, and in exchange for his silence. That's 2 new crimes for him, not covered by the commutation, and 2 new crimes for Bush.
In addition, the pardon power at the time the constitution was drafted did not cover the furtherance of a conspiracy to protect the Executive from future prosecution. It was intended to be an act of mercy for past crimes not related to the person granting the pardon. Just as no man may be a judge in his own case, no executive may grant a pardon in a matter that had put him in legal jeopardy.