This may be wishful thinking,
but If you have weapons engineer, can you spend the second target lock for your missile? That way you'd still be able to re-roll dice on ordinance?
Maybe its too legalistic but it seems to read "Attack (Target Lock): Spend your target lock" but if you have two target locks, you'd have the one on your target ship, so that lets you start the attack and then the second target lock is still "your" target lock so you could spend it?