Stallman's fear is that Microsoft will use its software patents to force open source C# implementations, and applications, underground.
Any move toward bringing C#, which Microsoft developed and Mono, which Microsoft supports, into the center of the Linux community must therefore be resisted.
The problem is not in the C# implementations, but rather in Tomboy and other applications written in C#. If we lose the use of C#, we will lose them too. That doesn't make them unethical, but it means that writing them and using them is taking a gratuitous risk.
Stallman's problem is that this horse has left the barn. C# is both an ISO and Ecma standard. The fact it's part of a Microsoft-developed Common Language Infrastructure is irrelevant at this point.
Microsoft can end this controversy with a press release, and a simple legal document, promising not to enforce software patent rights on the software. But how likely is that? [poll=106]