To each his own! Jim could pull a switcharoo on us but I don't think so. Maybe with a character but I don't think with Dresden or the grey council as a whole. I don't see it turning out that the Black Council is actually a group of wizard fighting for the greater good.
Oh, Im confident at least some of them are fighting for A Greater Good. Whether everyone will agree with either the "Greater" or the "Good" part of that, who knows. At the very least we do know of one (Kumori) that is doing it for idealistic reasons rather than selfish ones. Hell, I dont think he's BC but Id be willing to describe Nic that way.
My actual prediction is that the BAT will be a big, ugly exploration of the Grey of Magic and Morality, lots of hard choices, hard Sacrifices, and Good Intentions taking things Southward. And the whole time we'll be seeing Elaine, off on her own, doing things we dont understand and that might seem downright Villainous if viewed with a bit of circumstantial Suspicion (which is the default for at least half the fan-base when if comes to Elaine). Everything will point to her being a direct Counterpart to Harry, Summer to his Winter, the Other Starborn, etc etc. At the end it will come down to Trusting Elaine, despite all his allies telling him not to. Jim said once that it will end in such a way where it hinges on Harry being the guy at the end making the Choice (dont quote me on phrasing) such that anyone else in his position would go the wrong way with it, that Being Who and What harry is at that moment is what would make the difference. In light of that sentiment: I think it will come down to Trust and respecting Free Will: and the most difficult way to do that is often just having to Stand Aside and trust Somebody Else's plan.