It will be great if Marketo can build logic to to handle duplicate address in Marketo and SFDC to look up based on Marketo ID, SFDC ID and email address.
This will iron out all the headaches on data duplication.
Can't you just do this based on either Marketo ID or SFDC ID? Both of those IDs are unique identifiers, so you should be able to merge duplicate records with matching IDs pretty easily.
Email addresses are often also used as unique identifiers on their own, so you should also be able to do that, but you wouldn't necessarily want to do that merge without a quick review of the records because you might have blank fields there or multiple folks from the same company who registered for an event but all used a generic company email address (info@ or sales@).