In the end I managed it using invisibility and forcefields, using a key to re-open the gate then leading everyone outside to deal with them one at a time, even the boss. I don't know if it's a bug, but if you lead the boss too far away from from his room, the red life bar for the boss fight disappears and the music stops so you get no visual indication of his health.
As far as I could tell, the boss doesn't drop anything other than the cannon, and as both the keys are on the floor already you could simply just pick up the keys while invisible and avoid killing the boss completely.