I know infestation exists as a way to balance mountain bases, but it's quite ridiculous that it doesn't have any counters itself.
The whole event is so ridiculous that I reload my latest autosave whenever it happens now.
Here's an idea: Ground Thumpers (300 steel, 6 components, require 1000W electricity)
Unlocked by researching Ground-Penetrating Scanner. Allows you to build thumpers, which regularly send seismic waves deep into the ground to keep the bugs away. Each thumper has a small radius (similar radius to sunlamp) that prevents hives from spawning in it.
Basically the opposite of thumpers in Dune (which were used to summon worms).
If it hasn't been fixed yet, you could always build wires all over every surface, as this keeps hives from spawning.
In a related note, I would love to have what you're talking about, and I would also love it if we could build a thicker roof so we could avoid raiders coming in that way. How hard would it be to build a roof of plasteel anyway?