The way I see it, it isn't lost content if you weren't going to join the guild in the first place. Its adding content to a character with a different view. I love joining thieve's guilds in the ES series, but the Riften guild definitely raises the question as to whether it should be around or not depending on the hero's perspective. With such deep connections throughout the city, the outcomes of rivaling the guild should produce an interesting outcome.
The guilds questline itself isn't the only content it provides.
No content is
lost, though. That's you're mistaken assumption. Does not doing anything for the Thieves' Guild make those places any more important? All making the Thieves' Guild immortal does is break the flow of the game - Every other "significant" power can be taken out and dethroned, up to and including
Spoiler Every Jarl, and even the Emperor Himself
Why are the Thieves' Guild and Maven Blackbriar given arbitrary immunity?
The thieves guild existing player intervention or not gives back story to the whole town, it's reputation throughout the world, it's atmosphere, Mjoll a backstory and reason for being, Maven and her ilk a backstory and a means to power, explains the Jarls weakness and the opinion of her people towards her among other things. Not every Jarl is killable you get rid of some depending on a choice you make, one of those replacements has a backstory and reason to power involving the Thieves Guild. The spoiler you mention involves a quest line (well it wouldn't as you'd have killed the DB) with a replacement lined up with a backstory.
The only was this is going to happen is with a DLC. Remove the guild and the town needs to change, power needs to shift, NPC's attitudes and dialogue need to change all paced and explained with a questline. Considering that doesn't happen now after the Civil war where camp leaders are set essential and everyone likes to talk about the ongoing war after you've taken the other sides leader and seat of power down, I can't see that happening so a DLC would at the very least leave me with a disjointed story, more pointless locations, another guilds questline cut shorter and less options.
Your making the mistake of thinking everyone plays like you and looks for the same as you do in the game. You want to kill them go for it, I not only want you and me to have that option I also want it to mean something and not just remove content and potential content for me and others.
As I say a well thought out option with replacement content and consequences would be great I don't even like the guild but I do like immersion and story, is Obsidian available?