Ora et Labora. Ideas for an alternative 2 player game ending rule?
The "extra turn" mechanism in Ora et Labora is something Uwe carried over from Le Havre. The intention is to avoid the The Kingmaker Dilemma, where a 3rd player is unable to win himself, but is able to choose between two actions that decide the winner. During the "extra turn", players can't be blocked out of actions, so each player acts in his own best interest to put the finishing touches on his board. There's a big stochastic factor in 3-4 player, where other players just happen to get in your way by accident; this is largely missing in 2 player.

Most of the points in the game usually come from buildings, and building them in a checkerboard pattern with settlements. Late-game buildings can be as many as 15-20 points just by sitting on your board between 2 or 3 settlements. If you're finding that 2-player games tend to find cycles which create lots of points (through relics, or wonders), you could try limiting them. Wonders are already limited at 8, but you could limit the relics (and pottery, books, and ornaments) to 16.