All the of the sources that I can find on the desegregation orders in the parishes surrounding Baton Rouge seem to be 1969, three years after this school (in it's present form) was brought into being.  This source on page 5 shows East Feliciana (where the school) is located to have a desgregation order with a date of 1969.  If it is a segregation academy, the founders would have had to be able to see 3 years into the future.  Also, keeo in mind that the school claims lineage back to 1852 as shown on there official crest.