Deny the ability to add activities where child elements exist? i.e. if 1 of the 9 phases have a third level, deny the ability to add an activity to that high level phase (level 2)?

You can’t do it in administration of profiles, but rather you would just grant them access to the WBS nodes you want them to add activities into. This really is more of a longer conversation that would really need to be flushed out with a lot more detail with the organization's superusers and stakeholders. The administration of doing so can be tedious and create more work as each responsible manager in the WBS then has to be maintained.