You can execute the Marketo program and the lead or contact's Activity Log in Marketo will be updated. I'm not sure what will happen with the sync to SFDC though, if the lead or contact is owned by an inactive Salesforce user. When running Marketo's Merge service to mass merge duplicates the process failed in instances where the lead or contact was owned by an inactive user and we had to reassign ownership for all those leads/contacts to active users. Even if it works you may have other dependent processes fail - like sending alerts and interesting moments to inactive leads.
Your best bet would be to change the lead ownership to and active user (or users) - and establish a process for doing that when sales reps leave the company. As a fallback if it isn't obvious who should own the leads you could always designate or create an active SFDC user for ownership of these "orphan" leads and contacts and then reassign them later depending on whatever your rules are for lead assignment.
If can't reassign the leads, I recommend running the program first as a test on 2-3 of the leads owned by inactive users first and find out what happens.
Denise
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