Yes - this is definitely one way the problem can be solved, or at least managed better.
There was a feature recently added in NCrunch that can 
disable the auto-build for certain files in the solution.  This configuration setting was based off wildcards and could be adjusted at project level.  It is possible that a read-only-applying setting could be introduced along similar lines.
My first preference though would be to have this solved using a pre or post build step in your project.  The list of configuration settings for project files is getting longer and longer in NCrunch, and some people have mentioned they feel a bit daunted by it.  I'd rather use a new config setting as an absolute last resort.
If writing a script to do this in your build process ends up being particularly untidy, you might want to look at MSBuild's item batching features.  It's possible to create a custom MSBuild target that can batch compiled files over to command-line invoke or custom build task to set the read-only flag.