I don't think there's a way around this really. The upgrade may need to make changes to those tables (it won't delete data but an upgrade may need to alter the structure of those tables). Even if no changes are being made to those tables, code is being updated so it's not save for customers or administrators to have access to the website at the same time in case they experience inconsistencies or create integrity constraint violations.
Here's a guide on the the best way to upgrade from command line: http://devdocs.magento.com/guides/v2.2/comp-mgr/cli/cli-upgrade.html
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