The only autogenerated AssemblyInfo files are in cairo and in gtk-sharp's root, not inside other libraries like atk, glib, etc. Removing them will make MonoDevelop stop rendering a red element underneath each project.
Even though gtk-sharp cannot be built via MSBuild (yet?), it's better to make the .csproj reflect more closely what you get with the normal build.
This is just to be able to use MonoDevelop to browse the codebase, both custom and generated code. It is NOT intended to be used to build anything.