First, I'd simply live with the pulsing. Plenty of variables cause pulsing, and solving this now won't ensure that you won't have other issues later.

As for abrasively removing the anodizing, it's easy enough, but comes at the expense of brake track wear. It'll wear through soon enough anyway, so another reason to wait unless the pulsing is pronounced and you feel it becomes a control issue.

There are various methods to abrasively strip the brake track. One of the easiest is to buy some Scotch Brite, cut small pieces, and use strong thread or dental floss to tie to both brake shoes. Tie the ends tight, leaving the rest to do the work. Then ride in a parking lot, applying the brakes enough that you can feel the abrasive action. Be warned, the process creates heat, so stop and check rim temp frequently and rest to keep the rim below what will burn your finger. FWIW- I've seen people get the rim so hot that the Scotch Birte melts.