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.
I came to that conclusion from the apparent sequence of events as described in the third article I linked.
As I understand it this wasn't a case of "incrementally [falling] into doing something wrong" as Echnaton said back in 2013. Rather, Dunning got into contact with Shawn Hogan, found out about Hogan's cookie-stuffing scheme and, in Hogan's words, blackmailed him into getting Hogan's help. Later, according to Dunning, the two of them worked together to make their scheme even less detectable by eBay by various means.
This, to me, reads like Dunning was acting with full awareness that he was doing the wrong thing and trying to cover his tracks.
Like Dunning, I think it is odd that he got singled out to make this a federal case...
It appears he wasn't singled out - Hogan was charged as part of the same operation. According to this article (
http://www.businessinsider.com.au/ebay-the-fbi-shawn-hogan-and-brian-dunning-2013-4?op=1) Hogan and Dunning were eBay's #1 and #2 affiliates, respectively, in terms of earnings.