You want to prevent Marketo from updating certain fields within Salesforce.
If you are interested in stopping Marketo from overwriting fields in Salesforce, you could change the Sync User permissions in SFDC. Specifically, the User Profile for the Sync User, inside the Field Level Permissions, you can remove 'edit' permissions for individual fields. If you want updates to this field in Salesforce to still sync down to Marketo, leave the 'read' permissions for the field. Please keep in mind that removing this edit permissions can cause discrepancies in data between Marketo and Salesforce.