Sounds like you are using the feature in a way that was never intended?
The option to allow customers to register themselves, but "require activation by email" was intended to confirm that customers register with a valid email address (and without typos) since they need to click the link in the email sent to them in order to confirm their email address is valid and finally activate the account.
Perhaps you are using this trigger to send the activation email to an internal staff member instead of the customer? Which is not really the way it was designed - since it does not really confirm that the email address is valid and belongs to the right person.
While you could use your "plan b". Perhaps there are other options?
* disable the self registration, and instead add some text to say "If you don't have an account to access this store, please contact xyz to have an account setup".
* consider using the custom registration option for a custom registration process that suits your required workflow.