I suggest setting up a Migration using Migrate CSV. When Feeds is ready, it should be possible, but it looks incomplete at the time of posting.
Using the migrate code that you implement, set the accounts as blocked by calling
$user->block() per User import.
Block any anonymous user registrations, this will make new user additions possible only by admins.
In place of the user reg form, create a new custom form using Webform module or core Contact module. You can replicate the fields from the reg form of use to you there. On form submission, using a custom module including a
hook_form_FORM_ID_alter, do a check on the submitted form for email address and verify if it matches, then call
$user->activate() to unblock the user account.
Or if Rules module provides you the necessary settings through the UI, you could try the email address check using that, but this module maybe incomplete for this type of check at present.