First of all you should set up your blind schedule in a way that you have a reasonable chance of playing your tournament to a finish. So, if you have not been able to finish the tournament with 30 minute blind intervals, then try 20 minutes. Or start out with less chips for each player.

Secondly, instead of letting the chip leader take all the money you divide the prize money over the top-3. For instance 50%-30%-20%. Announce this before you start the tourney. If you have three people left, and one of them is a huge chip leader, then the other two are playing each as well as trying to just challenge the chip leader.

Finally, allow the final players to negotiate a deal on how to split up the prize money. As long as none of the players left in the game is excluded from this deal there is no problem with ending a tourney this way.