Originally Posted by Gregor-y
It's based on legal workings from he civil rights era where blacks (or whites registering them to vote) would be killed and local municipalities would either ignore the killings, refuse to prosecute based on claims similar to the current self defense explination, or put the killers on trial only to have a sympathetic jury (since jury selection was pretty heavily screened and blacks weren't allowed to serve) acquit them. Because a strict interpretation of the constitution does not prevent this, and because those actions were particularly egregious (though it had been happening for decades at a lower level), the only way to prosecute these crimes at a higher level was to interpret the killing based on a violation of the civil rights law, which was intended to prevent discrimination. In these cases the murders, being racially motivated, amounted to discrimination so federal law enforcement could get involved.
It's a long history spanning age-old local/federal and racial tensions that really hasn't been addressed as much as patched over by successive laws.