As far as Valve tinkering with Half-Life goes, that doesn't surprise me as the game is one people still play to catch up on the story and see what all the hype is about, especially with things like Portal(2) being loosely tied into it. Not to mention people find it easy to work with, for creating elaborate mods/their own games like "Cry For Fear" or some of the SCP game projects apparently. People still use it.
As far as the specific changes go, I have no paticular idea, but also wonder how many people would actually be negatively effected by this change, or if it's a tiny minority.
I use Windows myself (because it's there) but as an OS I've never much liked it. I haven't ever played with anything like Linux because I'm lazy when you get down to it. I'm guessing Gabe is probably anticipating a microsoft crash of sorts and trying to get prepped for a great changeover or something.
Who knows, maybe Valve will explain what they are thinking. At the end of the day they are the only ones who can answer the question, the rest of us can just speculate.