So tunnelers are a popular suggestion, and I can see how underground tidiness could be a big pet peeve, so I suggest a simple clean-up option: A "collapse tunnel(s)" function which fills up unnatural caves and tunnels created by tunneling monsters with the original stone/soil/what-have-you (and without changing the topography otherwise). And having it not work when the relevant tunnel has an occupant.
Now that we have constructed walls, this isn't really necessary, and it would end up getting used (incorrectly) as a tactical option: once you drive all the bad guys out of a section of tunnel, you can instantly collapse it and they can't come back. Additionally, it doesn't make sense to "collapse" a tunnel if, for example, there's nothing on the level above it.
Besides which, I like the idea of rock tunneling (by monsters or dwarves) being irreversible. Not everything should have an "undo" button.
I'm making a suggestion that does not interfere with your desires while also (hopefully) satisfying the other side, I think you should give it more thought than "I don't like it let's ignore it". Can you at least try to understand that there are multiple people with different playing styles here? If that's the way you want to play the game, nothing is keeping you from doing it. There is no scoreboard in Dwarf Fortress, so there's no reason to feel like ignoring a feature for the difficulty of it (which many players do now) is less fair than taking that feature away for everyone.
If you have a race (or multiple races) of creatures that tunnel, breed, create more tunnels, etc. and those tunnels are permanent, you're going to end up with an irreversible underground
mess within a few years, which makes no sense. In the real world, gophers don't hollow out the Earth, no reason for it to happen in Dwarf Fortress either. There is no reason to force the player to build wall after wall just to fill up gopher/worm/beast-of-the-ungodly/what-have-you tunnels.
Also, if the player has the ingenuity to force whatever hell-monster is tunneling into his battlements back up onto level ground, why
shouldn't he be able to collapse the tunnels it made? That makes no sense and just serves to value difficulty over strategy. If the tunneler isn't dead, it can start over, anyway.
I doubt there's much danger of this happening anyway, but I'd just like to say that "for the sake of preserving annoyance" is a bad reason to remove a feature.
It's not "preserving annoyance", it's "game balance". Editing the RAWs is overpowered.
Your problem with using the RAWs is more about making the game annoying than what the topic at hand concerns, i.e. making turtling less broken. As for anything else, I will avoid getting further into it because it branches too far from what this thread is about.