Yeah it's indeed a pitty that it starts from 3 players.
In the cooperative version it will be easy to incorporate it to play this with two players. Simply let the third nazgul be controlled by the player who does not control the witchking. In this way you don't have to change anything about the game.
In the competitive version it will be a little bit more difficult. In one way you could say that you both control 2 nazguls and you win if your combined total of VP exceeds those of the opponent.
For each playing only one Nazgul will be a little bit more difficult in terms of getting the balance right. But I wouldn't be surprised if some variant will pop up here that finds this balance.
We played with 3 past night and it felt like we had no chance at all to defeat this game. If there was only 2 players I don't think it's possible to beat all of the levels and win the game in the 9 turns.