The less sense you try to make out of Igiss' storyline the longer your brain will function.
Merely apply the ignore logic and common sense as we do for many other things on Freelancer.
(I personally think if they would have just sent out massive amounts of wine to Bretonia and Kusari they could have steam rolled in with 1/2 of their forces and won the day. Easy to blow up a ship full of drunks. More logical than a super huge fleet of ships running on oil doing it.)