PD will engage missiles automatically, no need for you to do anything. I do believe you need hardpoints deployed for them to work though.
Well that's a problem then, because you won't be able to charge your jump drive while trying to shoot them down.
I was talking about shooting the missiles with your main guns though, if you don't have PD you could try that.
I'll try to remember to do that, albeit when I'm blasting away from my enemies at 320 with FAOFF, 1) turning around is going to be slow and 2) trying to aim at anything is going to be insanely difficult, even at a stationary target. FAOFF is pretty finicky.
I've realized from people saying that silent running is a counter that you can go silent running and ALSO fire off a heat sink. This is two birds with one stone: you don't need to worry about overheating at all, allowing you to boost away full speed for a long time, and it also turns off your own heat sig while giving the missiles something else to chase. I'm thinking this tactic is going to be my go-to next time I'm in such a situation.