Okay so in the last episode of Book 2, Korra says that Wan was wrong to close the spirit portals right?
I was just watching Beginnings Part 2, the fight between Wan and Vaatu. Vaatu says that he was the one who broke the border seperating the spirit and the material world. Maybe Wan thought that because of this action, it had inadvertly brought about the near extinction of humans. So, at the time, closing the portals was the best decision he could've made. I feel Korra didn't exactly understand that.