The core OS architecture is not changing in Longhorn.
The CLR is purely user mode in Longhorn. That is anything running in kernel mode will necessarily be unmanaged. You can expect to see a managed kernel sometime within the next 10 years or so. It's a hardware problem as well as a software problem.
You will be able to write fully functional Windows applications in Longhorn in entirely managed code. The need to be unmanaged in user mode will be rarer than it has ever been before.