Good question Naor. In our instance Acquisition Program is mapped to SFDC Lead and Contact fields (e.g. mkto__Acquisition_Program__c), but that field name is not displayed in the list of Lead and Contact fields in the SFDC Setup | Customize | Contacts | Fields, yet other similar fields like mkto_si__Last_Interesting_Moment__c are displayed.
A possible workaround would be to create an SFDC field (Acquisition Program 2), make it visible to the Marketo Synch profile and then create a smart campaign with a Change Data Value flow action that updates that new custom field with the value of the Acquisition Program field using the {{lead.Acquisition Program Name}} token.