Can I delete the data that was synced?

Yes. Disconnecting a store stops the sync, and deleting it removes the synced orders, refunds and transactions. Your product records and the cost rules attached to them are kept on purpose, because those are your work rather than Shopify's, and deleting them would throw away the history that prices your past.

Deleting the whole account removes everything, including those rules. Before you do either, the export in Settings gives you every dataset as files you keep.