The idea of gods having flaws is a distinct similarity to Greek/Roman mythology, in which devine entities behave as humans would, becoming arrogant in their infinite power. It's really a brilliant move on Adam's part, as this flawed god idea means there is some depth to the character they warship, as opposed to a infinitely perfect being - mortals cannot understand perfection, so why try to make them?
It all adds to the "shades of grey" theme used it in whole story - sometimes, the leader's choice isn't the best, the Protagonist isn't invincible, the brave and valiant move will fail, and in the end it always ends the same way.
I also find it interesting how El-Arairah, basically the god of bravery, cunningness, trickery and most importantly, survival, is portrayed as flawed, whereas Frith (life) and the Black Rabbit (death) are portrayed as static, mechanical and righteous entities. This leads me to think that the rabbits' mindsets are that the elements of survival are flawed and imperfect, but life and death are constants in their universe. Which, if you know how rabbits live (and die), makes perfect sense as means to explain and justify the tragedy of being everything's prey - a thousand enemies.