I understand this goes against everything that Marketo is about, trying to keep the integration synced, BUT I have been asked if it is possible to deduplicate records on the Marketo side, since we are responsible for those, and we are getting charged for duplicates on the Marketo side, while Salesforce does not have near the financial reason to deduplicate records, nor is my group responsible for Salesforce. Anyone have any ideas on this?
I'd start here: Find and Merge Duplicate Leads - Marketo Docs - Product Docs
If you have a lot, the manual process is very tedious, but you will note that Marketo does offer a service at the bottom that can get you setup on the right foot. I haven't checked in on pricing but online offers up $3,000 for the one time service. Source: http://www.alp100.com/handling-duplicate-leads-in-marketo/