That having been said, it looks like the school really screwed the pooch in how they treated the kids from the historically black school.
The story obviously fails to give enough of the relevant background. That said, my quick first reaction is that if there was a combination of two schools with significantly different academic profiles a wise administration might have chosen to go with co-valedictorians and salutatorians for a year or two.
Yes, that would be a bit awkward since the emphasis in a newly realigned school would have been on building a common identity. But if one school was far more rigorous academically than the other -- a fact that would be known to all the students and that would have been apparent in every class in the new school -- an accommodation would be in order. Straight A's from one school don't necessarily mean the same thing as straight A's from another.