I tried to read that article, but I didn't want to invest the time. It was lengthy... However, I would look at it like this, if a pardon was given, it was done for one of 3 reasons;
1. It was justifiable. i.e., the facts used to convict were impeachable.
2. There was a quid pro quo, i.e., Bush received something in return for the pardon.
3. Or there was some national security interest served.
Given what I know about the man, I tend to believe number 3. However, this is just my opinion and I have nothing to prove or disprove any of the potential scenarios.
However, this is one questionable pardon. How many did Bill issue on his last day in office? How many were "questionable?" How many of Bill’s are undeniably "number 2?"