I have a couple leagues I have run for years and one I started ten years ago that is now up to $500 entry fee. I solve the problem by selecting two associate commissioners to review all trades, conflicts, disputes, rule change proposals etc. They help me keep perspective on things each year.
I have finished lower than fourth, and it happens, especially when decimated by injuries and holdouts. I also play in WAY too many leagues and varying formats. This year is my first year in an auction format, and I jumped into a big puddle for my coming out party...Dave Dorie is one of the team owners lol. Regardless, owners need to keep their perspective during the season and understand that everyone is attempting to win, and each may come at it with strikingly different philosophies and game plans.
The bottom line is, as long as the dealings are honest, let 'em go at it. A commish shouldn't be penalized for being the commish.