It would be nice to have some options here, e.g. keep the 'Use MailPoet to customize WooCommerce emails' but be able to disable the rest of the WooCommerce stuff, like automations.

Totally agreed. Even better would be to break out those features into their own add-on plug-in instead of needlessly bloating this plug-in with irrelevant secondary functionality. That way you guys could focus on developing regular email marketing functionality which should be priority 1 instead of getting distracted with woo commerce fixes.