I'm sure someone else has suggested this, but what if instead of killing worlds, each world was contracted? You could reduce D3 by 8-16 of the 32 conferences... and with a little programming you could move coaches and players from one program to another, at least allowing some continuity for existing coaches. So if you decide, for example, that the Empire 8 is undersubscribed across all worlds, you could contract it, and then in Wooden you could move the players and coach from the strong Vassar program in that world to a conference that is not contracted, to a program that was a sim previously. So the Vassar owner's experience is that he wakes up one morning with the same players, only his school is now, say, Emory (and his conference mates are different). I don't know what the need is for this at the D1-D2 level, might be none, might be just dropping 4-6 low-D1 conferences or so.
Lots of problems (moving players is probably not too hard, but moving prestige might be; hard to synchronize the contraction across worlds; conference relationships would be essentially impossible to keep in contracted conferences), but might yield a better game in the long run without too many people quitting. Willing to be shot down on this; fire away.