...In order to fix this, I would have to lay up a couple of layers of glass then micro on top of the counter weight where it is a little thinner.
That's more of a band-aid than a fix. The rudder is the reference structure, and there's nothing wrong with it. It's the VS tip that isn't contoured quite right to match the rudder, and it's the VS tip that you should fix if you so choose. The fiberglass tips are quite floppy until you bond in an end cap, and you can significantly alter the contour of the tip by how you shape the end cap. That would be the "right" solution.
And in general, bonding fiberglass and fillers over aluminum structure is possible (we do it for the canopy), but it's better avoided when possible, in my opinion. It's prone to future cracking and separation.
...Probably the only thing to be gained from trying to fix it would be some unnecessary weight. ...
Actually, I have to point out that added weight would not be a factor in this case. The fix Marc proposed would add weight to the end of the counterbalance arm. So if you were really worried about those few grams, you could drill out the equivalent amount from the lead brick, thereby restoring the original weight and balance of the rudder.
Still, I would agree (yes, just my opinion...) in this particular case forget about it and build on. It's no worse than half the RV's out there, and there are plenty of other more important things to worry about. You can spend as much or as little time as you want to get things a little bit closer to perfect, but since you never reach perfection, prioritization is the key. Very high priorities (things that can kill you): aerodynamic, mechanical, and structural integrity of the airplane. Medium high priorities: weight reduction, drag reduction, maintainability, etc. Somewhere waaaay lower on the ladder: minor cosmetic imperfections.
But I will say this about this particular problem, and in general: if you do decide to take action, do it right. No short cuts, no band aids.