Playoffs don't decide the best team. There is a large luck factor involved in any playoff system, including fantasy. If you want to decide the best team, play Roto or go by the regular season record. Most understand that playoffs do not decide the best team in the league, but they create excitement. If the playoffs cease to have much excitement because of a league-wide benching, then it should probably be changed. That is just my opinion. If something is broke, fix it or become the BCS.
Secondly and most importantly, a commissioner is not a dictator, he is just a commissioner. If the majority wants a change, then they should get it. Sticking to your guns may be admirable, but all you will do is upset people. It is their league too, in fact it is more their league than it is yours. Your job is to handle lopsided trades, inactive teams and collusion. Your opinion is just one of the many when it comes to league changes.
About the actual issue, I don't see the problem. Football does it, Basketball does it, Baseball should do it and there are plenty of leagues that do and manage to retain competitive balance. It really isn't that big of a deal guys, this year was quite ridiculous. I watch quite a bit of baseball and have for some time and this sort of thing always happens at the end of the year, but this year was much more than usual.
I say go with whatever the league decides. If most of them want the change, then it should be changed. If your league is really that competitive, then it shouldn't matter when the playoffs start.