The best way to do this is to use ILDASM to disassemble the managed binary, which will generate the IL instructions. Then recompile that IL source code in debug mode using ILASM, when you fire up the Visual Studio debugger you will be able to step through the raw IL.
ildasm foo.exe /OUT=foo.exe.il /SOURCEilasm foo.exe.il /DEBUG
I’ve written a blog post about this topic at:
How to debug Compiler Generated code.