If these guys want you as "commish for life" then step up as their leader and voice your opinion as an owner and also as the "leader" of this well established league.
You could try the other variation where there are 2 wins to be had each week... 1 for the straight heads up win and the other for the top half of scoring in the league that week. This allows the team who loses to the top scorer in a week by a point to still go 1-1 for the week. If they're worried about getting screwed, even though they may have accumulated the most points throughout the season, then give a larger payout for most points in the regular season.
There is always going to be the bad beats when you lose to the highest point getter in a week and the other guys are squeaking by with 20 points. But there is nothing that you can do about it when you set your lineup. I hope that your looking to start the highest point totalers on a weekly basis, not worrying who your opponent is starting.
Unfortunately, alot of guys do not take well to change...but if they're willing to radically change your playing schedule then a playoff system shouldn't be out of the question.
GOOD LUCK!!!!!!