I do auto body restoration for a friends body shop. Can you look at the back side of the panel? Many times, pin holes are a sign that that whole area is compromised and rusted pretty thin...I've not had very good luck trying to weld rust hoels shut as they will either blow a larger hole due to the panels being thinner from rust, or the weld is real nasty as the rust on the backside pulls into the puddle creating a real mess.
Your best bet is to cut the area out and weld in a patch section...will be a longer lasting repair IMO.
BTw, the technique I find that works best on thin materials is to pulse the arc on and off with your finger. This keeps the heat low and distortion down, but keep a wet rag handy to cool the welds as you go. When welding patch panels I recommend welding about 1/2" to 1" long beads at a time, cool with wet rag and move to another area...skip around to minimize distortion.