OK, after some reading, here is how I would, in terms of rules, implements this scenre:
I found some "drone missile" stats in Rigger 5, so I would used that and simply consider the 3 missiles launched are part of the rigger (pilot of the airplane shooting) them "drone set". Which means he can use his RCC and some autosoft with them (still need to check this out, I'm quite NOT on top of the all drone stuff).
The missiles will be "chasing" the VTOL. If they get to a "nearby" range, the rigger - if getting desperate, would have the option to detonate them and do half dommage. If it can get closer "boum" (full dommage - with the right amounts of cheat on my part for them, NOT to die).
The impact of the Air Spirit in the battle will be reduced to a malus to the manoeuver - at least until the badly hurt Mage deals with it (if he can). As a simplification, I'll use the Spirit level for the malus on the dice pool. It can be a lot in term of malus, but my PC bought an atmospheric sensor [that I've ported from a SR4 book, Arsenal I think], so this sensor will mitigate the effect).
Regarding hacking the missile, here is my understanding on how the rules would apply here. Given the speed and the distance, I don't think the missile can effectively be in a PAN (noise will either make the PAN useless or the missile too sluggish to operate).
However, missile does need to be "on" as they are getting command from the rigger. So if they are online, they can be hack. No PAN would mean device rating as FW, most likley a device rating of ~6 for such military grade objects. The decker will be able to either attack the missile (brute force, bricks'em or add marks up to be able to reboot) or follow the connection trail (i think there is an action for that in Data Trail) up to the Rigger's plane, mark it and Spoof Command from there.
(Sidenote about that, if the decker can mark the RCC, he would be able to send, in one action, a Spoof command to all of the missile, right ? That is again my understanding, maybe faulty, of the rules)
An other aspect of this scene, is that the rigger driving the missile can only do it if he keeps a lock (cf target lock rules in Rigger 5) on the PC's chopper. But does it means that if the PCs managed to break the target lock, the scene ends here ? Is the source of the target lock the rigger aircraft or the missile (or all ?) ? Would the PCs have to break one by one the target lock, before truly "escape" ?