This post is not saying "we shouldn't make anything relying on any non-free software because all software should be free software." It's a pragmatic post saying, "look, it's likely that all of the man-years going into C# free software will be lost when we can't run that software on our machines. So write it in something that we'll be able to use on Unix forever." If someone chose a proprietary framework with official implementations on Unix systems, this post wouldn't say that those are bad as well.
For an example, check out the .NET reflector. By default, it lets you convert between C#, VB.NET, (Managed) C++, and CIL. You can also get plugins for IronPython and so forth.
http://www.red-gate.com/products/reflector/ (it's free)
The program the poster was referring to is actually a disassembler, taking Microsoft IL (assembly for the virtual machine) and converting it to a .Net language. So you might;
- compile C# to Microsoft IL - decompile the IL back to IronPython - use that as the basis of a CPython version.
Why throw the baby out with the bath water?