This exact situation came up in my game a couple sessions ago when a player was trying to certamen an NPC to stop him from carrying out his wizards war.
Well, we have seen about 10 additions to the code, it's not quite so easy to say what is and isn't in the Peripheral Code. Since Tribunal votes are protected, and a covenant's charter is protected, it seems logical to me that covenant votes would be protected.
But it sounds like you guys have made your decision and moved on, I hope it works out well.
And you are of course entitled to have your own Tribunal rulings in your campaign. Indeed, IME every campaign needs some of these.
Ahm - AFAICS and without any new Tribunal rulings, functioning of a covenant according to its charter is protected from certamen among the charter's signataries only, if certain precautions are taken within the charter, and the charter is ratified by a Quaesitor. Without some Tribunal rulings of your own, non-signataries are not bound by a charter in any way, and need not respect its provisions about certamen.
Once you have made up your mind about your Tribunal's stance on certamen and covenant charters, you should also follow through with it.
But please always keep in mind that this thread was started by a request to summarize what's in the books about certamen, not what happens in individual campaigns. So positing without evidence Tribunal rulings which modify the rationale and outcome of a main example in the main rulebook is ... well ... deviating from the subject.
Kind regards,
Berengar
I recognize your points, they just don't feel right to me. Not out of an anachronisitic democratic ideal sentiment, but just that it isn' the kind of disputes Certamen is intended to decide.
I don't have any further argument to offer, others have already spoken more eloquently than I have. So I guess all I have left is to challenge you, Berengar, to Certamen to force you to rally to my point of view. 
I think we've all long since ran through the 2 paragraphs specifically dealing with the legal force of Certamen in all of ArM5, and are now well into the "welcome opinions".
So I'll continue to supply them, if that's ok with you.
I agree, but it seems to me that there's no way a Tribunal would uphold a Certamen refused by a member not wanting to violate his oath to his covenant.
You don't need to. I fully recognize that ArM5 leaves everybody ample space to introduce further local Tribunal rulings on subjects which do not feel right to the troupe, and above that also to modify the degree of enforcement of the peripheral code - and to a lesser degree even of the Code - in the Tribunal and the Order.
But before one does so, it certainly helps to consider what precisely is already in the books, and hence forms the basis and background of these modifications.
If this is the general opinion now, perhaps Cuchulainshound will excuse everybody, if we now switch to explain our local Tribunal rulings, their motivations, and how they fit with the published peripheral code?
Kind regards,
Berengar
Hey, you're not getting out of the challenge that easily.
Berengar has refused the challenge.
Fruny now needs to declare a Wizards War on Berengar ,
or face a punitive result at the next Grand Tribunal. 
Should be enough GrandMasters & Masters for a quorum.
No. No. you have it reversed. Berengar refused so he has automatically lost, we were all witnesses to his demise. He can refuse to accept the result and face tribunal or declare wizards war on us all to remove the witnesses. 
It seems much of this comes down to the same philosophical split that many RL politicians and lawmakers struggle with, which the writers of the American Bill of Rights and such debated long and hotly: Does a document which outlines "Rights" imply that anything not specifically prohibitted is, therefore, a Right, or are those merely the few that are guaranteed, and others may be banned as locally preferred by lesser authorities? If something is not specifically "illegal", is it therefore "legal"? (And, further, is it "right" or desirable?)
Also ignored by some is the fact that any mage who dislikes a charter can simply, IC, opt not to join that Covenant. From a meta-game standpoint, this is more awkward if the Characters are all joining a Spring Covenant with a distasteful charter (ie, the Players must now build a different character), but if that's the saga, that's the saga, and the Player should have asked before building that character. (Same happens with certain other character types (esp certain Companion concepts) that clash with a given saga plotline or covenant realities; the SG is well within their rights to veto them "just because", and the Magi running the Covenant are likewise under no obligation to accept them IC just because they carry a "Player Character's Card".)
Just as it's selfish and anti-social for a single Player to expect a game to revolve or contort around their preferred character type, so it's non-productive to have fixed expectations regarding any "interpretation" of the rules or game-world that is not explicitly and clearly outlined by canon (and even then!)
I don't think, as has been suggested, that Certamen is "broken", but, as with so many things, it needs to be refined and defined by each Troupe as best fits their needs.
(And, yes, feel free by me to go off on related tangents at this point. I think three and a half pages is ample sampling and exchange of opinion, thanks to all for their contributions.)