My thought is that you should have only a certain set of servers that have the free transfer access.
Also you might want to limit the amount of invading alliances that can enter the ark, and boost the cooldown for transfer, after a transfer to an entire 2 weeks. This would be to discourage super clans from destroying servers, then doing the same things in 12 hrs. If they have to sit around for 2 weeks on a dead server that they killed, they will get bored with this unsportsmanlike practice real quick (and hamstrung if they have to divide their forces).
I have seen in a game called Warcommander an instance of what everyone is talking about: a massive collation of players from another country invading a server and taking it over. How they are able to gather as many of their random countryman (in this case Italians) together as they are for raiding some random foriegn server I HAVE NO IDEA. But its something guilds from many countries do for some reason.
Long story short. I feel like such crazy massive mega raids can be fun, but it should not be allowed on absolutely all servers within a particular game mode. Otherwise you are handing the PVP (and for all I know quite possibly the PVE) of the game over to the elite super awesome alpha tribal alliances of cheekiness. If you allow it on a special set of PVP servers than it could be an awesome gamemode in its own right.
You could even have home arks that only people within an alliance can be in (basically PVE), that are a base for raids into the PVP servers. So these Arks would act as capitals that either can never be raided, or only raided when certain other arks had been captured. Basically a "Risk" mode in Ark.