Looking back at this now, I think if I faced a similar situation I'd probably try to exterminate the guards near the wormhole first, taking advantage of the others not "waking up" until you actually approach their guard post, and then send in Raid starships for the warp gate (taking care they don't fly too close to any other concentrations of enemies). That way, you probably only have to deal with 100-200 ships at a time, which is a bit rough when you're outmarked but manageable. You could also try to lure the first clump of guards through the wormhole intentionally so your turrets could cut them up.
If I remember right, at the time I didn't realize you could build force fields to block the wormholes the AI needs to pass to get to your homeworld. You can, and I would do that, usually putting the command center underneath it to save on the unit cap. Logistics and military command stations can also add a lot to your defense. That choice is discussed really well in this thread: http://www.arcengames.com/forums/index.php/topic,8169.0.html