Ok, let's go through this one by one.
1: Server focus.
Yes, it would more then likely become a focus of the server but would that necessarily be such a bad thing? It would add such a new and interesting aspect to the game that i think it would be great for the server.
2: Changing.
I pretty much new what i was suggesting when i did suggested it. Yes, it would alter PvP, but not in such a way unlike how cannons did, with airships, it would be more like moving cannons. Now, if you mean the architecture of factions literally, then yes, it would require you to build something of a air dock. If you mean it more metaphorically, then, a restructure of any faction hierarchy would be as simple as appointing a trusted member in the faction as a "Skycaptain" or something along those lines. Yes, a new form of Griefing would be introduced, but this can simply be taken care of by setting up a law that says one is not allowed to just park and leave a blimp in another factions territory. Yeah, there would always be people who break this law, but there are ALWAYS be people who will grief, and more then likely they have/will be punished. Now, what belongs to a faction is just that, you built it, it's yours, but, this can add a very interesting element to thieves and bandits. While the components of a airship may not be valuable, the collection of all them together make it a valuable item, and as i have learned (the hard way mind you) theft of valuable items is allowed. (also, in a side note, who is actually going to log off on one of these things close enough to the ground to be jacked? Just park the sucker at sky level, and you will be good.)
3: Trial period.
While more then a month would be something of....overkill, i think that a 3 week -4 week trial period would be a good idea. Why? Simply because that would let people get failure with the idea and allow them to get some time under their belt for them to figure you if they like the idea or not.
4: The end.
Yes, it would change Massivecraft in huge way, but I personally don't believe it would be for the worse.