I feel the main reason beacon persistence is brought up is because said player inactive beacon interferes with others players ability to build, and get their desired results.
Say a city or guild, you're building, and decide that you want to further expand your place, but the beacon next to you, is empty and blocking your way, or it's in the way of a new city landmark or common area, it would bother 1 or more people. But that wouldn't always be the case. Say your beacon is in a stranded area, no beacon to see in the horizon, no one would have anything to hold against you. So why should your beacon be removed?
True that with the guild system, there should be less problems inside a guild or city with unwanted beacons, as most would be the guilds disposition, or whatever, guild system is still being worked, so we never know.
Just as @Cookviper mentioned, I don't feel the player should lose progress, just because they stopped playing. But there should be a way for the beacon to be removed from it's place, with everything inside it, returning to it's owner. And maybe, just maybe, keep it the same way as it was, I don't know how hard it will be to program and code, so if it's gonna be a pain in the ass, please don't consider it for 1.0 release. As I know you have your hands full with so much stuff already.
And about the time playing protecting your beacon from being removed, the only gripe I have against it, and it's because I've seen it happen in other games is, players logging in, and been afk, to generate "play time". Again nullifying the purpose of the system.
I'm all in favor of players not losing progress, as well as I'm in favor of removing beacons that are in the way of others plans. Let's be honest, no one likes to see a dead beacon in the vicinity of the city or guild you're in, and if the player isn't active anymore, it will be removed, with the items inside, returning to it's owner. But if you have a beacon somewhere no one frequents, then who's there to complain?, who's affected by it? Let it stay there, peacefully and quietly.
So @Karokendo mentioned this idea to me, and I took the liberty to make some "upgrades or changes" to it
Have a voting system be implemented. Instead of making the fueling system harder.
Beacons will only have the option to vote up a beacon for removal, after the beacon is not longer active (has no more fuel) and it's voted by players after crafting a special voting tool (tool will be hard to make (rare materials), and it stops trolls from trolling that easily).
Beacon will be removed after the player hasn't responded to the issue and it's reached enough votes (maybe 5?), or it hasn't been protected by another players votes to keep it.
Everything inside a beacon, gets returned to the player it belongs. Only the empty plot will remain, for other players to take.
That way, only inactive players beacons, that disturb others, will be removed, and the ones who're affecting nobody, even though it's not fueled, will remain as they were left.