Farms can pretty easily be abandoned if need be. Just wall it off if it's a security risk.
Also, climbers seem not to be much of a problem for me... maybe it's just because I'm not getting sieges, but my outer ring (which I am totally prepared to abandon, and mostly consists of roadblocks and cage traps to catch the random critters I might want to tame) doesn't seem to get much trouble with climbers. I think they only climb once all other options are exhausted, so a tree laughing at your 2z-high walls isn't a problem if you have a hallway filled with weapon traps just open and inviting all the gobbos in.
For the caverns, my simplest method is to just punch a hole in the ceiling, then pave a floor over it. No fuss no muss.
Want a cave critter trap?
The path is a "shortcut" through some mazey sections of the caverns, making it attractive to wanderers. It has a wooden door and a tame guineacock to attract predators and building destroyers. The ramps have retracted 1-tile bridges over them, and the cavern is sealed from my fort via drawbridge. I just check in every now and then to see what I've caught. (GCS rushing into my trap in this image.)
Whole thing takes a couple dwarves a month to complete at most, and that's mostly time waiting for bridges and levers to be built/connected.
Anyway, you should likely be capable of monster-proofing your cistern if you take a bit of time to do so. Presuming you're pulling this water from a brook or something, since you're not talking aquifer or caverns, then all you need to do is have a "U-bend" that lets water come up from below via hydrostatic pressure, and put a grate on the tile that the water springs up through. Put any pressure cutter (diagonal path) before the U-bend. That stops any building destroyers, isn't too laborious, and lets you put up windows to your heart's content. (Bonus if your cistern is near a natural river, so you get vermin fish to spawn there.)
Remember to build roads or floors in your plumbing to stop tower-cap growth!