To remove scratches = wearing thru its useful life , ahead of time, since you have to bring the rest of the metal down to the depth of the scratch.
I Say Ride it, get new pads , or if too far gone, replace the Rim or Wheel.
Is there a way to do that without impacting the anodizing
Buy a Bike with Hub or disc brakes..
I got a bike with Hard anodized rims , and rim braking Improved once I scoured thru the anodizing.