Sadly, it seems that Dunning's actions were motivated only by greed.
I am not quite sure what that means or how one can determine the sole motivation of another.
From the perspective of more information, this is what I see. Dunning had a contract with Ebay that called on him to act in a certain way. He worked with employees or contractors of Ebay who were aware or encouraged him to act differently, to the detriment of the company and perhaps other marketing affiliates like himself. He may be right that representatives of Ebay knew about it and approved. However his actions were essentially conspiring with employes or contractors to violate the contract he signed to the detriment of the other party. That is one clear definition of fraud.
ETA: It seems in my non-professional opinion, that the fraud rises to the criminal level because it was to the disadvantage of other affiliates. Had it been a pure contractual issues with Ebay, it
may have only been a civil case. Fraud to the disadvantage of parties not in the contract seems to be a sound reason for the criminal case.
While Dunning may be right that it was a common and known practice, that is not a legal defense. The contract is the term, not what everyone else does. He would have to produce documentation that would be tantamount to a contractual amendment as a defense. Something he apparently could not do. Like Dunning, I think it is odd that he got singled out to make this a federal case, but it did fall under the very broad definition of federal wire fraud. However, claims of selective prosecution or legal overreaching no matter how justified, are no legal defense. The lesson is a simple basic of business and law, if you have a contract, stick to the contract or get it amended to allow what you want to do.
It is all a shame, because I have been a big fan of his podcast. It has been a good learning tool in my family. The public message of the work has been greatly diminished by the flaws of the messenger.