High school metal shop has been a long time ago, but since when does stainless have a high carbon content?
Have you sent your pic and an inquirey to the manufacturer? Wonder what they'd say?
I wouldn't bother polishing brake rotors. Kind of silly if you think about it. Just ride the thing. Let the pads shine things up.... much more fun.
There are many alloys of stainless steel -- 300 series, austenitic chromium-nickel alloys, are partially magnetic and soft and hard at the same due to the eutectic nickel content. Machines well as long as cutters, speeds, and feeds are just right -- otherwise tends to tear instead of cut. Very corrosion and heat resistant, but too "soft" for brake rotor use -- prone to galling.
400 series, ferritic and martensitic chromium alloys with varying carbon content, are tougher than 300, but much less corrosion resistant. Function well as rotors, but surface iron crystals are prone to etching if left exposed to moisture for an extended period. The discolored area is actually pits in the metal and will have to wear down or be ground down to get rid of them. The decrease in swept area in this region is so slight it is unlikely to cause a change in feel, but water will get entrained in the pits causing a slight pulsation on initial application in the rain. Other than this, all it really does is look bad.
By the way, I never use WD-40 or any other lubricant on any brake component -- it's difficult to get it all off, especially if there are pits in the surface. Just wash them as you would the rest of the bike and dry them with the blower side of a shop vacuum or a hair blow drier. When parking it after a wet ride, get the front wheel off the ground and blow dry the rotors, preferably after retracting the pads slightly. Remember to pump the brakes before going on your next ride!