The message that an email already exists while attempting to checkout as guest tells you clearly that this customer is not a "guest" anymore, but that he has a (Joomla) user account with that email address.
So, you should probably provide the possibility for existing users to log in to their account. The alternative is to delete existing customers' user accounts, but be aware of the implications and possible consequences.
See also here :http://www.hikashop.com/forum/checkout/872332-cant-pay-for-product-email-already-in-use.html#175915 and in other similar threads.