So I set up a turret that has autofire enabled. I gave it a weapon that locks on and has homing missiles (tested and works as a unit). My problem is that since the turret fires instantaneously it doesn't give itself time to lock on. What can I do about this? locktime 0 makes it not lock on at all.

I don't have my mod tools on me at the moment, but consider the following parameters: TurnRate, WaverRate, and WaverTurn. If you incrementally increase the values of either one of the following parameters (I forgot which one does it exactly) in the missile's ordnance ODF, then it should automatically home in on targets without having to lock on first. I hope this leads you in the right direction...

So does that mean I should remove the lines pertaining to lock on in the launcher odf?

They are independent of each of other. And not that it matters since your auto turret won't be able to lock on anyway.