I think they're expanding to Linux entirely because they want to expand to and support Linux, not because of any competitive pressure forcing them to retreat to Linux. A couple years ago they expanded to Mac, and this is just a natural extension.
So there is the possibility that MS could turn around and say "No, Steam is banned from Windows" in the same way that apple would with the iPad.
This at least gives Valve the power to threaten MS with "FU, we're going to Linux and taking HL3 , Portal 3 and CS:GA with us"
This seems pretty unlikely. I doubt there are enough linux gamers in existance to justify what this investment will cost.
Unlike OSX, where Valve probably didn't get as much traction with Steam before the mac app store was released, Steam IS the primary gaming service for Windows PCs.
It's an opportunity to produce a Gamers Distro based on a solid Distro. They could piggy back a Ubuntu LTS, and focus on a subset of well supported hardware.
Valve already do, but it's not disclosed to the public how much. So I can't see how MS doing so would make any difference.
Edit: I thought you were talking about MS taking a cut of game publisher's money, not Valve's. It's such a far-fetched scenario given everything we know about Windows 8 it didn't register in my mind.