I don't really understand the question. Maybe I am confused... but.
C# and the Common Language Infrastructure (CLI) is to .NET what C++ and compiler is to KDE.
.NET is a huge sprawling monster covering a massive amount of APIs, hooks, functionality and whatnot that is designed for a entire application programming environment.
Were as on the other hand C# and CLI is a open specification, published by ECMA on behalf of Microsoft, that defines a language and language runtime environment. The reason MS did that was to promote the language... they WANT 3rd parties to use it and establish it as real language and runtime environment.
So, no. The "promise not to sue" only covers the language, not .NET. These are two completely seperate things.
This is why things like Tomboy are safe for Linux distributions. (at least as safe as any other language). It (AFAIK) has no .NET at all in it. It is pure Gnome and does not use any Microsoft technology besides the actual CLI, which is a open specification.
However Tomboy being safe does not make all of Mono or all Mono programs safe. One of Mono's goals is to create a .NET compatibility layer so that it is easy for commercial folks to port their applications over to Linux.
In that case Mono is in the same league as Wine and Winelib. They are designed to do the similar things, which is to provide a development environment were users can build and run applications in Linux that will also run fine in Windows, and make it easier for developers to make Windows programs cross-platform.
So it really is a good idea to split off the ".NET" portions of Mono into seperate packages so that distributions can keep the "pure gnome" side of things seperate and be safe from Microsoft's patents.