Two-player balance?

By Dvil, in Chaos in the Old World

Does this idea work for balance with two players? Basically my friend and I were bored, and decided to play. I knew it was only really balanced for three or four people, so we came up with this. Basically, each person controls two gods. It worked, sort of, and we enjoyed ourselves, but I got to thinking about the balance. It was our second game, so we had Khorne and Tzeentch together (as the most and least simple to get the hang of) and the others together.One thing we did was to house-rule that allied gods didn't attack each other in combat.

So basically, I thought it might be a good idea to come to the more experienced members of this board and ask whether you think this could work, and which god combinations seem most balanced?

A friend of mine and I ended up playing just one on one, and it wasn't so bad. We still would have rather played Horus Heresy, but we haven't gotten up the scratch for it.

I'm very interested in this as well. I prefer 4 player games, but getting that many people together isn't always possible.