Whether micro-kernels are the way to achieve it or not (and possibly they might be) I think there's a need from the security PoV to move away from the idea of an all-powerful root user. The MO of a lot of exploits is privilege escalation.
The functions of root need to be split. One function would be to allocate user IDs. Another would be to allocate storage space. A third would install applications. None of them would have the ability to read or write anything other than what they need to do. If an application needs to access file space it should do so in a space allocated for that particular application or at most a class of applications.
Instead of calling a common kernel service an office application, for instance, would call an office data storage service with some means of checking that the client was a registered office storage client in addition to the check that the user had access rights according to user, group or public settings* with nobody else.
The storage service might even be able to check file format. It might provide versioning. What it wouldn't do would be to provide read access to some malware trying to exfiltrate data or hold the data to ransom. Such malware would not only have to impersonate the user but also the application.
This division of responsibilities might have a performance impact but that would be the cost of security. As things are we currently see security being sold cheap in terms of convenience and performance. It needs to be given a higher value.
* Or some other ACL