Maybe true for unoptimized code. However, Java and C# compilers have received years of work to make efficient use of their respective VMs; standing on their shoulders makes some sense.
You won't see the C# compiler inlining functions (even though the CLR does _way_ better with large functions and doesn't handle inlining well). It won't propagate constant expressions. You won't see it transforming recursive functions into loops. Does it even remove unused variables?
All the optimizations that C# really relies on for performance are handled by the JIT, and any compiler following the same patterns will get the same enhancements, plus the ability to emit better IL than C#.
That said, I'm still unconvinced it's easier to emit MSIL than C#, and I'm rather well versed with MSIL.