You could polish them and then use a polishing or protective agent on it to prevent rust. Not sure what type of material you are working with, but assume it's stainless steel. I tried this on my sdr with what I would consider stunning results. I think these headers are stainless and or titanium.
When I first polished these, they appeared Chrome in color, but heat will turn them into a golden chrome color due to the material used.
This is what they actually look like without polish, but actually much worse due to being on the bikes undercarriage:
This was done 4 months ago and there has been no sign of corrosion or rust. It has not even been washed since then. The headers stay remarkably clean in this state. All you need is a drill and one of those polishing kits from the hardware, oh and some elbow grease!
I will probably end up doing this to my 500, but haven't due to me being too lazy to remove the wrap. I can't quite discern exactly what material these headers are made out of, but from appearance, the material looks the same on both bikes. Still, I would caution you to find out the material in case yours is different.
It's probably evident that I'm no expert on rust or steel for that matter, but thought I suggest this as it's worked great for me. :thumbup: