The first four Zero-G troops that the Assault Shuttle launches will attack you. You should just ignore these guys for now. Shortly after these are launched, two other Zero-G troops are launched - these are the scumbags who can make your day pretty bad as they'll try to identify Aeron. Destroy these two ASAP. Note that they have multiple waves (three waves if memory serves). Next you can either attack the remaining Zero-G troops or the Assault Shuttle.
When the Strike Cruiser exits hyperspace, you can move to intercept the fighters if they get within 1.5 kilometres and if Aeron isn't finished yet then pick her up after you've wasted the first flight group.