If you have a method of distinguishing leads of the parent company from leads of the child companies, you could use segmentations to classify the two. In your scoring and syncing campaigns you could add Smart List logic so that it would exclude leads that were owned by your child company based off their segment. Segmentation and Snippets - Marketo Docs - Product Docs
Amy, if the child companies are completely independent and would like to keep their Leads separate from the parent company, then I would create a new Lead Partition with a "dupe rule by Partition ID". That way you allow for duplicates across Partitions (but not within Partitions). This means you lose the 360-degree view of the Customer because the same Lead can be in both Partitions, but it sounds like that is fine in your case. You then set up a Partition Assignment rule (Admin > Workspaces > partitions tab) so that all SFDC leads flow into the Parent company's Partition.
To prevent accidental syncing of Leads to SFDC in the child company's Workspace you can set up a validation rule in SFDC that will reject new Leads, unless they have a particular field value (which could be as simple as a check box "okay to sync"). In your parent company Partition you will have to set that check box to true before you call "Sync Lead to SFDC". It is no possible to remove the "Sync to SFDC" flow step in the child company's workspace.