The part you are concerned about reads: or to different punishments, pains, or penalties, on account of such person being an alien, or by reason of his color, or race, than are prescribed for the punishment of citizens,
In the plain language of this section, the antecedent controlled by race, nationality or color is different punisments, pains or penalties.
The depravation of constitutional rights applies to anyone. The same civil provisions in USC 42 § 1983 were part of the case against Nifong, etc. the plaintiff's of which were very decidedly white.
The structure of 242 seems subject to different parsings, but if it was used on Nifong, I’ll defer to your parsing of it.