We are able to Merge 2 SSR [Salesforce Sync Records] in Marketo via Merge API. Choose the Master record and pass that Id as Winner id in URL and Other records as [Runner ids] in URL Parameters.
Merge API :
Method : POST
URL : Marekto Endpoint/rest/v1/leads/{id}/merge.json?leadId=1324
where
id = Winner id
leadId = Runner id [Comma separated values]
Reference : https://developers.marketo.com/rest-api/lead-database/leads/