I can sympathize with you on the very poorly thought out housing system, though I do understand what SE intended. I'd like to think that they just overlooked some of the consequences of the systems they set up, however, there are so many 'bad' ideas mixed together that it's hard to believe that they didn't see at least some of the repercussions long before implementation.

The private quarters being deleted while you were away, I think, is something that they overlooked. It's a feature that was added after the static housing system and as such tied directly to it. If they'd thought it out more fully they'd have made it more like a license that you purchase (once) and also required that you belong to a FC with a house in order to access your private quarters (though they should still exist even if you're between FCs). It's just a small instanced zone that should be tied to your character and not the FC, let alone the specific house the FC owns.

I have no idea how much work it might be to untangle the system to allow for this, but it certainly would be possible to do. I don't recall exactly, but I think that they did mention adding a different type of housing that might essentially be private quarters+ (I think there was some gardening available) that is not tied to a FC, but to an individual and would be mostly instanced. I think they said they'd be like apartment buildings -- one large building with some basic common amenities but mostly tons of instanced private rooms. It's been a while since I read anything on it so perhaps I'm full of it or seriously misremembering things, but hopefully they're working on at least adding reasonable housing options even if they don't plan on outright removing the expensive (to the characters and servers) and poorly implemented housing that they have now.

As a current home owner, I really wish they would just say, 'Sorry for the ongoing trouble. We know we messed up really badly with the housing system and we're unfortunately going to scrap everything and redesign it from the ground up. It will all be instanced so that everyone can have a house if they want one and we'll do our best to refund all gil that people have spent on the current system and to give people a chance to reclaim their furnishings.'