They can be destroyed in two ways. Destroying all six of the armed pods will set off a chain reaction which detonates the base. Also, if your aim is good, you can destroy the base with a single shot by hitting the reactor core at the center of the base. This shot can be difficult to make but it is definitely more stylish.
The bases are heavily armored, immune to even heavy weapons, and they are armed with a range of weaponry. Sometimes they launch tight-flying formations of ships led by an ace pilot. Destroying an entire formation will earn you bonus hazard pay.
When you have destroyed all Centaurian bases in a zone, you will collect your hazard pay and have an opportunity to buy new components for your ship before entering the next zone.