Welcome to AirForums Chris!
On our first Airstream (1964 GlobeTrotter), had Zolatone that was in great shape with just a few scratches & minor areas of damage as you describe yours - certainly not bad enough to warrant re-spraying or painting over. I went to a local train model hobby shop and bought the tiny little bottles of model paint in colors like the flecks in our Zolatone and a tiny little brush and dabbed the colors on to blend with the Zolatone. I also "painted" replaced rivets the same way. You could not see the repairs once done.
The key is finding the colors in your Zolatone and keeping the sheen down - a lot of the model paints were "high gloss" (which didn't look right), but I found the model paints had a lot of flat "neutral colors" that blended very nicely with our Zolatone. It just took patience & looks of little dabs letting them dry in between so as not to look muddled.
As I recall though, '61's may have the older Zolatone which is more of a solid color with more random flecks...ours was the newer style that was more solid flecks. Regardless, I think the same approach would work. Find colors that match an faux-finish to match the Zolatone colors/pattern.
On our second Airstream, we stripped years of paint off the Zolatone and re-sprayed new Zolatone - so we didn't have to go through the faux-finishing as in our '64, but I have touched-up replaced rivets in the same manner.