Another, of course speculative, motivation may have been that the destroyed records could have thrown existing land ownership into legal doubt.
EDIT: The article speculates a cover-up. I'm speculating a make-this-messy-problem-go-away action, perhaps by someone who'd have to deal with the mess as opposed to someone who'd be embarrassed by it. On the other hand, I'm not denying that it's a cover-up.
The article focuses on the potential harm to one or more prominent families' reputations; as you deduce, this kind of evidence would not only harm reputations but may also complicate land ownership.
"My suspicion is that in and amongst all those now destroyed records, was a paper trail associated with one or more now-prominent, politically connected NC families that found its wealth and success through theft, intimidation, and outrageous corruption."
EDIT: The article speculates a cover-up. I'm speculating a make-this-messy-problem-go-away action, perhaps by someone who'd have to deal with the mess as opposed to someone who'd be embarrassed by it. On the other hand, I'm not denying that it's a cover-up.