Thank you for the feedback.
I've played with various methods on our sandbox environment and deleting records from the core_store table does indeed cascade through, so this works well.
1 note for anyone else doing this; after you've removed all your stores, you wont be able to remove the superfluous core_websites records until you perform a complete reindex (FK constraint on pricing tables).
After trimming all but 2 stores and 2 websites the overall database has shed 30% of its size, with the biggest win in the core_url_rewrite table - down from 1.25 million records to a relatively lightweight 325k! Category page load times are now on average 2 seconds faster. Shed those superfluous Magento stores Mage People :)
Thanks again for your help.