The fix requires a level head and being clever with the smallest amount of coding. Though to toss my two cents in this is how I'd do it:

First I'd change the color of each campaign name on the campaign list based on who is winning (I.E. has an Emperor) in that campaign. This will allow for an "at a glance" determination for where (or if) you select a home server, but more over it makes it easy to know where your faction has an advantage/disadvantage. Bandwagoning wussies that just want to win can confidently choose their campaign, and those of us who want to murder them like the scrubs they are will know where to find them: Win-Win. What this does is give rise to cross campaign cooperation within ones Alliance.

To support that previous notion a global faction chat would be another simple yet tremendous game changer in terms of getting players where we need them, when we need them. Big fight for Emperor going on in Bloodthorn? Make the call. Rally the troops. Make it a fight worthy of remembrance. As the system currently encourages server migration, people are going to be playing hop-scotch on the campaigns either way, why not turn the problem into the solution? The bandwagoning wussies can still run, but now they can't hide.

Then I'd hard lock home campaigns. You want to migrate? Pay $10. End of line. Then, I'd tweak the "Guest" feature and change it to a "Mercenary" feature, which would work identically to the guest feature, but with two small changes: 1) No time restriction on how often one can move servers, 2) by invitation only (I call it a "hiring system"). "Hiring" a "Mercenary" would be costly in AP, say 10k per player, so a four player party queue would cost the inviting player 40k AP. What this does when viewed against the above options is seriously constrict the mobility of bandwagoning wussies (whom no one wants on their side), and enhance the mobility of good players out looking to scrap. Suddenly players are policing the campaign balance and a dev's life just got a bit easier.

Naturally the above feature is weighted in favor of the winning faction as they'll likely have more AP than the loosing faction, so the tweak we make here is a cost based on primarily the number of capture points held and secondly on population, all the way down to being free when you hold nearly nothing and it's pretty much just you and your pet mudcrab defending that nothing. These will be the avenues for players who want to fight to get a fight, and put the other "P" back in this "PvP" system.

tl;dr version:

We create a scenario where players can intelligently choose a home campaign at a glance, but they're stuck with that choice unless they shell out $10 to change that. But, they can get invited as often as they want to other campaigns at the cost of AP of players in that campaign, or freely to campaigns that are ghost towns for their Alliance. All of which made fairly easy via a global Alliance chat. Then if the dev's really want to utilize the game architecture, "hiring mercenaries" to your campaign could be as simple as adding the functionality in the LFG tool.