Unfortunately the machine cannot think, and therefore does not know whether you need the plasma arc initiated, or not - only you know that.
The solution is to use a different code when you need the arc, to when you move rapidly. If you use G1 when cutting and G0 for a rapid, then you are there. Include the M3 start up routine in the code for the G1. I take it that it does not matter if the initiate arc code is used, even though the arc is already on.
You could also include the code for M5 (if that is what you are using), to shut down the code BEFORE a rapid move, to avoid cut where it is not wanted.
In that case, your job would be completely automatic.