Unless a case could be made for a racial aspect, then 242 does not apply, and we have to go with 241
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.