If you absolutely have to use aspnet_compiler, then I think you answered your own question there:
I've also thought about maybe making the cmsdesk a separate application that only needs to be compiled after a new hotfix has been applied.
That is like what Kentico 8/8.1 does to help reduce the build time, but instead it has all the Kentico controls/pages in a single project and just your custom code in another project. Download it and install to see what I'm talking about.
We're not using the aspnet_compiler, we use a web application project and have MSbuild compile all our classes, etc. We have our Hudson CI server building all the Kentico 8.1 projects and our custom projects with MSBuild, it takes less than 30 seconds for everything including all our unit tests, this is on 7200RPM HDDs.
Realistically, how much time are you saving by pre-compiling with aspnet_compiler? Most of the commonly used controls are compiled very quickly by the server on the very first visit. I've never seen a big enough difference between the two styles to warrant using aspnet_compiler with any of our projects, just my experiences.