Create a simple ratings system for commissioners
I have played in may private custom leagues in Yahoo! Fantasy Sports and once in a while I run into a bad or shady commissioner. If a commissioner out-and-out cheats there is a mechanism for reporting them, but if they do something like change the settings after the draft or make otherwise questionable decisions, owners are just stuck.
A simple thumbs up or down rating by all of the league owners at the end of a season would probably do the trick. Bad commissioners would be even more rare, and good commissioners would be recognized for their efforts.
True...bad commissioners could still operate. But the point is they would be competing against commissioners with good feedback. It's like Ebay...you generally avoid sellers with no feedback and value those with lots of good feedback.
All a bad commish would need to do is create another ID and they would be back in business.
may = many