Wow... two different things. Multi-faction and PvP.
Multi-faction at launch
Yes and no. I would be hurt if I had a pared-down Federation just so the Cardassians and Ferengi could be included. As much fun as PvP can potentially be, its not the core of MMO gaming, and I don't think a whole game should be modified to accomodate PvP, ever.
That said, PvP should be included at launch. I recommend the Maqui as a playable faction. Ships that are PvP-enabled, whether PC or NPC, could get missions against the Maqui. Of course, the Maqui would have PvP constantly, between each other, between federation and any other factions that get added. Unlocking one could be easy... you could have a "low key" Maqui recruiter in each area of the tutorial/starfleet academy... once you finish you can go with him and booyah... your PvP all day long.
PvP
Bad PvP is abusive and not fun, providing only psychological payoff for the victor, with no actual enjoyable gameplay for either party. Griefing is, in short, taking the fun out of a game... if a game is not fun, then it becomes useless. It should go in the trash, imho.
We've seen weak implimentations of consequence based RP fail to address griefing... they test the limits, so you have to draw the line close. There's no such thing as "oh it was only one time violating the neutral zone." You break the rules, you have a problem instantly. No one is going to forgive you or take it easy on you... especially if you don't take it easy on others.
It's Open Consequence-based PvP that's most faithful to the fiction. You CAN go to Kronos and start shooting, but there are consequences. If you cross another faction, not only does that faction have a problem with you, but so does the Federation (or your faction) because you almost started a war! That's loss of prestige and a bump down in tier missions, a missed promotion, probably and on top of that you have the offended faction gunning for you as well. Multiple offenses, especially of the same type might move your faction, especially Starfleet, to demote you. Other factions, as they come on, might have other disciplinary functions for those who abuse PvP.
At that point, a person, griefer or otherwise, has to really think, is making this breach worth losing this much on this character. Of course, if a mission is generated, all bets are off, at least as far as your faction goes, because you got the mission from them... and PvP missions wouldn't be hard to come by, because they'd be set up to create, as much as possible, fair matches.
PvP is great when its fair, and it folds out of and into a storyline. But the free-for-all camping foolishness has to have ZERO tolerance, especially for factions like the Federation. The most important thing is that fear of PvP should not change players' actions. When PvP is out of control, people begin to play in unrealistic repetitive immersion-breaking ways in order to win and get ahead in PvP. The only way to keep PvP in check is with swift harsh consequences for breaking the rules... at the same time, you don't want to artificially enforce the rules, as that has the same immersion breaking effect for many.
Multi-Faction done right
As aluded to, different factions have radically different skillsets, technology, mission types and advancement chains. I think its conceivable for a well funded game to pull out three major factions at launch, Klingons, Romulans and Feds. That's conceivable... I think trying to do any more is greedy and is asking for low quality gaming... where faction is just window dressing. That's something worth shooting for, and that's something worth waiting six months to a year for. I say launch with Fed and Maqui, give us Klingons and Roms in 3-6 months; Cards, Ferengi, Andorians and Borg in 6-9 months; and a bunch of "minor" factions: Orions, Breen, Tholians, Jem'Hadar, Bajorans, and Xindi inside a year. Each with notably different gameplay and advancement options. If the foundations for each faction are different, starting with unfinished factions is not really an option, because then you have an unfinished game, which is not as fun as a finished game.
I don't think the time difference will be a huge problem in balance. Each newly playable faction will have been present in the game from launch, and have tons of active NPCs of varying purpose and use, even from faction to faction.
I'm also of the mind that different factions should have different PvP rules. While Borg and Federation have no in-faction PvP, the Maqui may be a free for all. The Klingon may have clan-based PvP and the Romulans may have a deuling system.
War
I think war should be reached cooperatively by both sides. Taking certain mission chains can lead to a battle with a given faction. Outside of mission based skirmishes (which can be pretty large)... a battle involves a raid of some sort undertaken by one side against a resource or vital area of the other side (target based on which mission chains are used)... it can be a surprise to the frequentors of said faction (perhaps given 2-3 minutes warning) but would not be to those running the storylines that have created the battle. These can be relatively huge, and many many players can be involved.
I think continuous wars should be controlled by the NPC faction heads, and feed into well organized GM storylines and have real meaningful mission creation teams put on them to design additional content suited to the conflict that is immersive.
Conclusion
I'm all for good PvP, I'm all for having all the factions. I agree PvP should be in game at launch... but hamstringing the game, or the entire universe, just to cater to PvPing is a bad idea, and strikes me as very shortsighted.