Allow the deconstruction staff to rewind destroyed natural structures. Catcoon stumps, tall bird nests, hound mounds, etc, should all have a way of being brought back especially if a world is thousands of days old. It can cost the whole staff if it needs to, but they shouldn't be gone forever.
I understand people want consequences for reckless behaviour but that doesn't necessarily mean consequences cant be paid for. It can be as expensive as you need to be Klei.
Edit: Place the construction staff on the moon pedestal to make a construction staff. 5 uses.