Originally posted by Blaise Russel
The Meson warhead was only intended to destroy the Knossos portal, as they reckoned that without the portal's stabilising influence, the node would collapse anyway. They were wrong; while being stabilised by the Knossos, the node had become stable in its own right, and no longer needed the portal to keep it usable.
Exactly. Command thought that without the Knossos, the Shivans wouldn't be able to get through because the subspace tunnel would become unstable again. However, either it already became stabilized on its own, or the Shivans were able to get through before it actually started to destabilize.
Clearing out the fighters would ensure that the bomb squad got back safely. Also, detonating the bomb would also kill you and anything in the immediate vicinity, not allowing Command to take that course of action. Besides, the Shivan fighters would probably be too fast and fly away before the bomb goes kaboom anyway.