I answered my question by trying it out in a test environment and found that it is not safe to delete the item from the fusion table datastore. I deleted a different entity in the datastore and have replicated (instead of fixed) the issue
Moral: If you delete the fusion table in the datastore, ODK Aggregate will report that the datastore is corrupt (because it is!).
This is a separate issue it seems than the one for this thread. I created a new thread with the problem.