I think it is difficult to avoid your situation. If lead already exist in database, from SFDC and if you import a list in Marketo, it will update the SFDC records which are already part of Marketo.
I will suggest to re-import the list with additional field values which you want to update, though it will update the same SFDC records, but additional field data will be updated in same record.
Also, best way is to clean the duplicates to avoid such rework.
Unique URL Field = XYZ (list)
and it will bring in the right records.
As Kapil suggests, this is a serious dupe problem. I'd reach out to Lean Data or RingLead to help.