I've posted before that I think only Merlin and Ancient Mai were actually able to attend the meeting that expelled Harry. Moreover, given what we know about the Senior Council operates, Merlin controlled the proxies of all non-attending SC members. We KNOW that McCoy, LTW and even Christos (whom I think is not BC, actually) were damaged in the fight. Liberty was there, but we don't know if she was injured.
There was a great deal of controversy at that meeting -- at least judging by the fact that Carlos had been screaming at people during the meeting.
I don't think that Merlin kicked Harry out to flush out the Black Council. I don't think Merlin really wants to admit to the existence of the Black Council, and honestly, it don't see much evidence of their acting up recently. After Harry's "death" it's been Fomor this and Fomor that. Perhaps the Black Council receded to allow the Fomor to occupy everyone's attention. Now that Harry has destroyed the Fomor -- and he did destroy them -- the Black Council will get active again.
I'm inclined to think that Merlin kicked Harry out thinking that he could control Harry by enticing him with re-entry. However, it could just be as simple as not wanting someone with so many divided loyalties in the White Council. After all, Harry is beholden to/mixed up with Heaven, Hell, Odin, Winter X 3 (Mab, Molly, Lea), Summer, Demonreach and the White Court of Vampires through various debts, favors, obligations, grudges, etc.
If you think about it, it's quite a mess. I'm told that networking is a good thing, but perhaps not always.