Well - here's a thought.
Make those guilds 'inactive' - so they aren't losing anything, and also don't show up on the leaderboards at all.
But the instant someone logs back in, the guild is back. It could be at level 25, because of decay, but it'll be back, and the owner hasn't lost their money that they used to buy a ship.
But tell me 'if you don't play enough, you'll lose your guild and ship'. I'm out. I'm not going to let some game company choose my amount of playtime, this is a game, not a full time job. Pay me, if you want that. I'm not going to let a company STEAL my money if I buy something but don't play their game enough to meet their standards. Ever.
As for cost...
A F2P player can make that much free turbine points - but then again, those f2p people who never pay are the ones who usually quit the game fairly quick. Someone who has put real money into the system is more likely to stick around a little longer.
Right now you can game the system and farm renown on the 6 (?) servers and get a free guild in less than a week (probably more like a day), then off you wander to a game you like more.
But really in the end, that's a personal view. I think turbine is stupidly missing out on more profit, if the game is in such desperate need of cash flow, then they need to look at what sells.
And seems to me, everyone wants to be king
(and really, don't care THAT much, it's their company - if they didn't change the price, no skin off my back)