Yes! We now have the option to merge records in Pardot. For more information see our Merging Prospects article.
Previously, we recommend adding information to the Notes field in Pardot (which is also a custom field in the CRM) about the second record for the prospect, maybe including the link to the other record. Also you could manually opt out one of the records if you know for sure the prospect prefers the other email address. However, now you can merge two records (their field values, activities, etc) into one Pardot record.
Salesforce.com/SugarCRM Note: When a record is merged or deleted in salesforce.com or SugarCRM, Pardot is told to stop trying to sync the prospect (to prevent it from recreating the record in the CRM). It will only start syncing that prospect again if the CRM record is undeleted or a new record with the same email address is later created in the CRM.
This is only the case if you already have a version of the CRM package with the delete trigger prior to deleting the CRM record. If a record is deleted before the trigger is installed, the records will be recreated by Pardot. To ensure the trigger is active, update your salesforce.com account with our latest AppExchange package or SugarCRM here.
As of February 2013, you now have the option to turn on (via automation rule) syncing for prospects whose lead or contact CRM record was deleted.