Just as advertised this modules sends every N days activation emails to all unconfirmed profiles on your site. If on your site there are hundreds or thousands of unconfirmed profiles and you configured the module to notify them every day then of course this would result in hundreds/thousands emails every night. So in that case it is necessary either to:
a) Delete old unconfirmed profiles
or
b) Set N parameter to a bigger value so it would notify unconfirmed members by portions every day.

Anyway see more to uninstall the module do the following:
1. Execute the following DB query to remove all records from DB:
DELETE FROM `sys_options` WHERE `Name` = 'confirmation_email_period' LIMIT 1;
DELETE FROM `sys_cron_jobs` WHERE `name` = 'auto_conf_emails' LIMIT 1;

2. Clean site's DB cache by clicking the "Clean db" link on the admin's dashboard page.