Hi,
You could change your checkout workflow in two steps: one with the login, and one with the rest. That way, the user wouldn't loose the credit card or address data when registering with an email which already has a user account.
There is no ajax system in place to do such check dynamically on the registration form when the customer enters his username. It would require some customization of the code of the view to handle that.
(The redirect plugin is to redirect the Joomla registration page to the HikaShop registration page. Not enabling it doesn't mean that the checkout will use the Joomla registration page. That would actually be impossible which is why HikaShop has to have its own registration form, like all the other ecommerce solutions for Joomla)