You can use separate flow for deletion to remove the records from target that no longer exist in source using replication task,so if that's your use case you can go with below approach :
Please let us know specific reason not use this approach.
You can also use the below to achieve this.
Way 1: Either use the target as dynamic lookup where you can delete the records in a mapping.
Way 2: Or you can use a joiner and join both source target using left outer join and get the Ids which are not present in target.
Step 2:then flag these Ids and then delete it from Target.
Way3 : If your source and target belongs to the same DB then you can create a SQL override query and then use it at source end to get these uncommon records and then use delete records option in target.