The SFDC is Deleted field can be used to identify a SFDC Lead or Contact which used to be in SFDC but was deleted and now only lives in Marketo. Typically the record is deleted from SFDC for a specific reason and most customers will honor the deletion in SFDC by also setting up a smart campaign to also delete the record from Marketo.
If you decide to keep the deleted record (SFDC Lead or Contact) in Marketo to nurture it, the next time the record flows through the SYNC Person to SFDC flow step Marketo will insert it into SFDC as a new lead record. A strategy should be in place to make sure you're not syncing/inserting records you really don't want.
If you decide to delete a SFDC Lead or Contact in Marketo only you should only do it if you have a custom sync rule set-up. Otherwise the next time the record is updated in SFDC it will sync again to Marketo with a new Marketo ID.
Here are the steps to delete a SFDC record which is syncing to Marketo:
Additional resources for learning about the Marketo integration with SFDC.