I like the idea of an Order Council. The Zoner Council has been a success, for the most part, though it gives ALL registered Zoners a vote. However, considering the less-anarchist more-military structure of the Order, having a set number of seats makes sense to me, though other Order players should be able to voice their opinions and concerns even if they don't get a vote.
While the Council would have no actual authority over those people who choose to ignore it, Order players should either decide to go with the Council or ignore it... Don't participate or pretend to go along with them only when they do things the way you want. If you don't agree with the Council or the Council's authority, stay out of it completely.
I see no problem with the Bs| getting multiple seats/votes, seeing as they are the main (and only) official Order faction, and being official should have a few perks, however minor. So two seats out of seven, or maybe three seats out of nine. They shouldn't have enough seats to push through any proposal with just Bs| votes, or even to tie it with just Bs| votes (though with an odd number of seats there should be no ties). I don't believe the Council should have less than seven seats, and more than nine is probably excessive.
With seven seats, give two to Bs|, one each for the two main unofficial Order factions (there are only two, right? If there are three, I'd say make it nine seats for sure), then three independents. The independents should be elected by the other independents (no nominating or voting for yourself).
With nine seats, give three to the Bs|, one each to the other main unofficial Order factions, then four (or three, if there are actually three main unofficial Order factions) to elected independents.
Once formed, the Council may wish to elect a Chairman to keep order (no pun intended, heheh) during sessions, much as the Zoner Council has done. Other than that, the Chairman may be given the authority to decide ties in the event of someone abstaining (which really shouldn't happen often), but none other than that and even that's up to the Council itself.
Anyway, those are my mostly unbiased opinions and suggestions. I only recently made my Order indie (though I had planned on it for some time), and have had almost zero contact with any of the Order factions and most independents (though I flew with the leader of the 42nd, she seemed quite nice). I do, however, intend to follow the decree's of the Council if it gets put together in a reasonably fair manner (which doesn't necessarily mean following ALL my suggestions... though I'd suggest it :D). As a matter of fact, my character only takes orders from the High Command, which I assume this council would try and represent (and could do well).