Rather than go off of novels or anything like that, I'm just going to start from what you've posted.
You have 3 groups, the Protectors, the Independents, and the Traitors.
The fact that you have deities you called "Independent" suggests that deities in your setting are not, well, dependent. This could mean the state of the world/setting does not affect them. It may be something they choose to treat as important, but it's not "vital to the survival" of the Gods. Or you could take the simpler meaning that those 3 deities are not part of either the "good guy team" or the "bad guy team". Regardless, the label begs the question of why they are independent. Yes, I see that their spheres of influence are in the "sometimes good, other times not so much" areas, but that's not the point. The point is motivation from the point of view of character logic. Think of the God as a person, and figure out why He/She goes for this deal.
The Protectors, same deal. In many ways the "sometimes good, other times not so much" argument could still be made, even with "The Just". "Justice" often isn't the same as "I got the result I wanted", and if anyone in the entire universe would be aware of that, it would be this guy. So what is it about the world and the worshipers that makes it worth being in basically a permanent state of war with another 3 Gods, and an always-in-a-state-of-flux neutrality with 3 more?
The Traitors... against what? "Traitors" not only implies someone working against you, but also that the someone working against you is someone you expected to be on your team. Okay fine, so what was the issue, what was the reason, why those you expected to be on your side decided to work against you? Remember, famous traitors in history rarely think of themselves as traitors, they think of themselves as patriots and martyrs. So just as with the Protectors, you have to ask yourself why they chose this result. Imagine a world where you could nail someone to a wall with a crossbow bolt through the head and have them not die, or go watch Liar Liar, and you can see how "The Traitors" could easily think of themselves as "no, we're the good guys".
In short, try to figure out not only what their motivation is for being who they are (in terms of sphere of influence and etc.), but also their motivation for making the enmities and alliances they have. Also try to decide whether the world and its worshipers are vital to them, merely a convenience, or just an interesting way to pass the time.
