Cookie-stuffing results in a significant cost to eBay and no additional revenue. No sane company would sanction it (beyond maybe turning a blind eye to someone doing the odd bit of cookie-stuffing if they earned most of their commission on driving real sales). Of course, plenty of sane companies that have departments that don't talk to each other about ongoing investigations and sales guys focused on next month's commission...

The program managers' role was to encourage an apparently very effective affiliate marketer to drive more real traffic to eBay, whether that was because they believed most of his referrals were genuine, thought they could persuade him to switch strategy to actually doing real marketing for eBay or simply adopting a business-as-usual approach whilst waiting for the fraud investigation to conclude. Either way, by his own admission Hogan wasn't remotely interested in investing in actually driving traffic to eBay even if they provided additional cash to support it...