In your alpha.txt (Alpha Centauri) or alphax.txt (Alien Crossfire), there should be a line:
Colony Module, Colony Pod, 0, 8,10, -1, None, ; Noncombat packages
Change it to "None" to "Disable. There will still be the default unit "colony pod", but neither you nor the computer will be able to put colony pods on new chassis.
This will work fine if you don't play with aliens. In that case, Sea Escape pods will still be generated when a coastal base is captured by a different species.
Sea Escape Pod, Foil, Colony Pod, Scout, 8, 0, 0, Disable, -1, 00000000000000000000000000
One solution might be to change "Foil" to any land chassis. The unit might either fail to be created, or drown immediately. Or it could crash your game. I haven't tested this. Alternatively, change "Colony Pod" to something else. "Transport" and "Supply" seem the most appropriate.
-RdF