When using Marketo with MSD, filtering the sync is a standard process. The MSD admin just has to create a field, name it "SyncToMkto" on leads, contacts and /or accounts and map it to Marketo. No need to call support. See Create a Custom Dynamics Sync Filter - Marketo Docs - Product Docs and the doc even explains how to set up MSD workflows to check / unckeck this field in MSD.
This idea is about having the same possibility on Salesforce.
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