Yeah, I'd just leave it. The alternating color is due to the spokes pulling on the rim and deforming it slightly. The pads then wear out the high-spots first. If you sand the low spots to accelerate the wearing of the anodizing, you'll cause a greater difference between the high & low spots. Then the pads will end up wearing out the high-spots even faster.
If you're talking about black streaks left by melting brake-pads, then some solvent like acetone/nail-polish remover scrubbed with a Scotchbrite pad will work fine. Don't get any on the tyre.