An interesting theory, but I think Cozarkian is correct about that WOJ. I think DonBugen also touches on the fact that JB is an award-winning, best selling novelist who is quite well educated on writing. Chances are (and if you think back to every book/poem/script etc analysis you may ever have done) that he will follow certain conventions of story writing for maximum effect. He may subvert them as well for gain, but the reason they are conventions is because they work.
So unless there is a really powerful reason for him to not use certain story-telling conventions, he probably will. In fact, he often does. There are some really great Dresden Files analysis' out there, and there is a mountain of info about story crafting that Jim himself has written. So I tend to use that as a base when constructing my own theories. And give JB some credit, his reveals are normally pretty good. I am sure when the time comes it will be a really good one regardless of who Cowl actually is.
And to answer your theory of what might happen, peregrine, if Dresden did recognise this background wizard at a Council summit as being Cowl (like the Wizard with the Curly mustache) - I think Harry being his normal level-headed self, would attempt to murder Cowl on the spot. And then settle for binding him when everyone had tried to restrain him. However, I would assume that the Cowl in your theory would have been preparing for such a thing (a la Emperor Palpatine), and turn it on Dresden somehow - perhaps even violently. But that's just my thinking.