The simplest way to ensure things are balanced is to make them the same. Give both sides the same powers, give them different names and change their visual effects.
I agree, that's pretty boring and likely won't give you very interesting game play. However, it's a good starting point.
Once you've got a good starting point, with good and evil having very similar "base" abilities, you expand. But you always expand both good and evil, in the same ways. Either give both sides similar abilities or give them equal but opposite abilities. Giving the evil deity a ability to create walls? Give the good deity an ability to remove walls. Giving the good deity an ability to heal over time? Give the evil deity a way to harm over time.
OK, things have gotten a bit more interesting. Deities don't have the exact same abilities anymore with just different visual effects. But, still kind of boring and not really there yet.
Next up is adding unique abilities for both sides. This is where you want to do some heavy play testing. When you're adding abilities that don't have a "counter ability" on the other side, it's important to play test. Obviously you'll want to play test with all the abilities, but these are the most likely to introduce unbalanced play.