Here's a wild one for you, and it's probably been said before, but why not explore it again.
There is no Black Council and never was. In fact, what Harry perceives as a Black Council is quite possibly several different things.
We know that the "Black Council" is a relatively new force, in the supernatural world. We also know they like screwing up everyone. We also know they seem to have members everywhere.
While Dresden muses that perhaps the Black Council is none other than Nemesis spread around, I think we can safely assume it's more than that.
It's hinted at that Margaret Le Fay was involved somehow, as she seems to be well known by lots of supposedly dark beings. However the Wardens and others never outright state she was evil, just that she was very like Harry and walked around the crumbling edges of the Laws of Magic and railed against the unfairness and lack of responsibility of the Council. She was friends with vampires, dark wizards, Denarians, gods, dark faeries and probably more. Just like Harry is.
Sure, Harry sees them as allies of necessity. Who says that Margaret didn't? Harry is allies with the Lara Raith, Mab, Molly (the Winter Lady and former Warlock), Vadderung (a shadowy being even when he is a good guy), The Erlking (King of the Goblins), Bigfoots (which some regard as monsters), the Summer Lady, the most notorious gangster in America - Freeholding Lord and now Knight of the Blackened Denarius Gentleman John Marcone etc. Not very different to his mother really. Not to mention he also is THE Warden of Demonreach (a place filled with dark gods, demons, Titans, and almost certainly Outsiders plus probably many other nasties). He also earned the respect of the God of the Greco-Roman Underworld, Hades. Not to mention he has an armory of divine weaponry from the Redeemer and now also the Eye of Balor. From the outside he looks pretty bad. Not to mention all his terrifying accomplishments and open defiance of great powers - including the White Council.
My theory is that groups like the Grey Council and the Executive Ministry of the Accorded Nations (some of which are actually on the Grey Council), are actually just cells of the Black Council. Harry is on to of these and just doesn't realise it. They all seem to have good intentions, sure. But clearly everyone has other motives. The end result is the accumulation of power - something Harry is doing naturally and exponentially. Even if he doesn't mean to. The Grey Council haven't really shown what they are up to...which is to say I suspect they are not doing what Harry believes they are.
What if Cowl and others are just another cell? Perhaps that's why it's called the Circle.
What if in the end, Harry goes so far down the road he ends up on what he thought was the Bad Guys team just to stop the Even Worse guys?
What if he is already on the team and just doesn't realise it?