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You could add all the duplicate records to a list and suppress that list in your campaign.
Once you've finished your dedupe project you could delete the list or remove the filter from your smart list to allow the leads to qualify for the campaign at a later date.
A solution such as Tara's is probably the most feasible. This behavior is an artifact of how Salesforce treats merges between records and there's nothing we can use on the Marketo side to determine whether membership is the result of an organic add or a merge.