Like when you warp in, the AI warps in help from a nearby planet? That's interesting. I don't think I've ever seen it do that. Are some neighboring planets on alert already, maybe filled up with a lot of stalking ships? You can always just take it a piece at a time. Send in your ships and beeline them for one guard post, accepting that they're going to be a suicide squad. Rebuild and repeat until the world is mostly cleaned up. Slow and messy, but it should get you there eventually.