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Marketo mandates an insert operation with the native sync if no GUID is yet associated with the Marketo-side record, so we can't force it to write into the webhook-created record. Have you looked into an automated merge on the CRM side? The synch will track these and merge the records in Marketo.
We're looking into merging the leads on the CRM side like you said. We though by removing the email in our smart campaign creates, we can avoid creating duplicates, and then each night we can simply deactivate the records with no emails and keep our Marketo created records.