It helps to look at the whole context of this sentence:
He was a dreamer in such wise, because he was a man who had, deep-rooted in his nature, a belief in all the gentle and good things his life had been without. Bred in meanness and hard dealing, this had rescued him to be a man of honourable mind and open hand. Bred in coldness and severity, this had rescued him to have a warm and sympathetic heart. Bred in a creed too darkly audacious to pursue, through its process of reserving the making of man in the image of his Creator to the making of his Creator in the image of an erring man, this had rescued him to judge not, and in humility to be merciful, and have hope and charity.
There are a series of sentences which follow the same pattern:
Bred in …, this had rescued him to …
What’s more, we note that in each of these cases, Arthur Clennan managed to, despite his breeding, become much the opposite of what he was bred to. Meanness and hard dealing? Honourable mind and open hand. Coldness and severity? Warm and sympathetic heart.
So what do we make of the creed to darkly audacious to purse? It must be a creed that is opposed to humility, mercy, hope and charity and we can see that in Dickens's demonstration of how the Biblical statement of man being made in the image of God has been inverted to God being made in the image of erring man. It’s not completely unambiguous about the creed too darkly audacious to purse, whether it’s the creed that was written but not followed by Clennan’s peers who preferred a God made in their image (and thus the creed that Clennan actually followed), or whether it’s the creed that Clennan’s peers did follow, that was exemplified by the preceding sentences. From the larger context, it seems likely that the creed to darkly audacious to pursue was the one that made God in man’s image and thus eschewed humility, mercy, hope and charity.