Like the App Store, the Marketplace is also governed by a number of terms, and in those, Microsoft makes it very clear - without mincing words - that it doesn't want any GPL'd code in the Marketplace. Article 5, point e of the Application Provider Agreement is what it's all about.
"The Application must not include software, documentation, or other materials that, in whole or in part, are governed by or subject to an Excluded License, or that would otherwise cause the Application to be subject to the terms of an Excluded License," it states.
This item is useless by itself, since it's not yet clear what an Excluded License is. Well, this term has been defined at the beginning of the document, and there, Microsoft makes it quite clear.
You can't really get much clearer than that, can you?
This is obviously not cool, but from the wording it becomes clear that this is not some super dastardly plan to destroy the GPL (I'm out of tinfoil, sadly), but more about covering their bases. Since Microsoft is a distributor of the software in question, it must also comply with the GPL; it must make the source code available upon request if someone so desires. I think Microsoft simply doesn't want to deal with that - in the same way Apple doesn't want to deal with it - and as such, prohibits you from distributing GPL code through the Marketplace.
While I'm actually quite sad about this, I do have to give them one prop for being clear, open, and honest about it. Of course, they'd get massive props if they came up with a way to make GPL code compatible with the Marketplace.