I think the NCAA was acting in good faith here. I don't think the NCAA has contempt for the U.S. military or for this ex-Marine, and I don't think the NCAA wanted to declare this guy ineligible out of spite or meanness or arrogance.
I think the NCAA was trying to apply a rule that wasn't designed for this situation, that the problem was compounded by the fact that a relevant clause apparently was deleted from the rule by accident, that the letter of the rule would have been unfavorable to the ex-Marine, that the NCAA struggled to find a resolution that would be consistent with the rules but still reach a fair result, and that the NCAA, in a roundabout, bureaucratic way, eventually resolved it in accordance with common sense and public opinion.
That seems to be most likely to me, but others may disagree.
I think the NCAA was trying to apply a rule that wasn't designed for this situation, that the problem was compounded by the fact that a relevant clause apparently was deleted from the rule by accident, that the letter of the rule would have been unfavorable to the ex-Marine, that the NCAA struggled to find a resolution that would be consistent with the rules but still reach a fair result, and that the NCAA, in a roundabout, bureaucratic way, eventually resolved it in accordance with common sense and public opinion.
That seems to be most likely to me, but others may disagree.