I've never cut polycarbonate, just done welding & marking of metals. I suppose the discoloration is due to the heat affected zone. The cure for that is increasing your peak power by using a pulsed profile with short-duration pulses with higher average power, and also increasing your traverse speed as you cut. With today's programmability, you can get very sophisticated pulse profiles. With enough experimentation, you might actually stumble upon some method that works.
You may also consider blowing cold nitrogen on the cutting area as you cut. Well, you could try AIR first (it's cheaper, use a venturi chiller), then move to N2 if air doesn't do well.
If the discoloration is due to a chemical reaction to the light wavelength, then I guess you're in a pickle.
It also occurred to me that you can contact the tech services department of the companies that supply polycarbonate (GE, DuPont, etc) and ask them if they have guidelines or experience on this issue.
