This hasn't happened on my SD but happened to every RSV Mille I ever heard of. It made no difference at all to the working of the clutch.
Replacing the fluid just resulted in it going black again shortly.
The generally accepted idea seemed to be that it was colour leaching out of seals somewhere. I don't know whether to believe that or not, but I can tell you that my Mille ran for 4 years like that and had no clutch problems at all, on road or track days.
Be worth getting your SD checked over though.
Mitch