Without really knowing the cause, I'm not sure anyone can say if polishing will make it worse or not.
I'd say call Woodwind/Brasswind tom and ask them. Or TJ direct. Describe what is happening and how it looks and what happened after you polished it. Have it there with you when you call in case they ask specifics like how long or how dark etc.
I'm guessing you don't have a regular instrument repairman? 'Cause I'm thinking mine would be my first call about this. I even called him when Brooks-May closed and had a Yami 580-something for $900-some (he very emphatically ordered me to buy it! And pointed out how good he was at spending other people's money, and BUY IT!!
) You know, if you don't have a repairman, that's someone you should shop around for. Best resource ever for your instrument. But probably look somewhere besides that store you hit today. Egads.
It's sad when folks get like that. I bought a GIANT lava lamp from a pawn shop, was working fine there 'til the bulb burned out. I found replacements, but it just made icky intestine-looking tubules rather than balls and globs. I contacted the lava lamp folks, who told me how to reset a lamp. Still made intestines. So she sent me a brand new replacement that is the most beautifully wonderfully magnificently active ballsy lamp I've seen! Incredible customer service. As in the definition of good good good! Too bad your shop's boss doesn't realize that making a customer happy (esp when it won't cost him anything more than possibly shipping) is so much better than stomping on the customer instead.
I have no idea how he thought he could pull off claiming the streaks are any sort of your fault.
Yeah, call TJ about this. And do keep posting how this goes for you. Esp if anyone figures out what the streaks are--good info to share!