Well, we tried this last night and it went really well, but not for any of the reasons I was expecting it to.
Loaded up some transports with bombers, blew through the wormhole and down to the command station, unloaded, popped the sucker, reloaded, and ran like hell. About 200 of 600 ships followed us back in a trickle, getting easily eaten by the defenses of the system they entered. The best part, though, was that since we already had the world surrounded on all four sides all the turrets went out of supply. The other map I've played on was so linear this situation never arose, so I wasn't expecting it, but a valuable lesson was learned about encircling dangerous targets! The fort was harmless, the turrets were dead, all we had to do was systematically pick off posts and their accompanying ships while avoiding that cursed ion cannon. When all was said and done we took the system fairly easily, all considered, and even got a mark I Ion Cannon as a prize in the doing.
Thanks for the advice again!
@Tusoalsob
Raid starships are an interesting possibility, I'll keep them in mind the next time something like this arises!