@nikolas, I believe we have achieved what we need to with the use of a couple of plugins (albeit I would still like to see this functionality in the native O365 plugin).
* Profile field based cohort membership
* Cohort role synchronization
The sync fields in the O365 plugins don't give you a lot of options, but for us the "Company" field just about does it. We have mapped this to both the "Institution Name" and a custom user field, and it is this custom user field that can be used to enrol users into a cohort using the "Profile field based cohort membership" plugin. You can then use an enrolment method of a "Cohort Sync" in the course, and et voila.
As a side option, we also use the "Cohort role synchronization" plugin to add a role to the users in the cohort, and this now allows us to show (or hide) course categories to those users.