I just want to thrown my 2 cents into the bucket here. This is clearly a preference issue. WWW is not deprecated, and if you *want* to use 'www', you should be able to. Just like you can choose whether to use subdomains or subdirectories. Or specify a quota for individual blogs. MU has awesome support for user preferences, I don't see why this should be an exception.
A good example is "browsehappy.com." It's just a web site that encourages people not to use IE. But does MU enforce you to use Firefox? No, because that would be silly and unreasonable. I also think it's unreasonable to think that everyone out there would want a system where you can't use "www" without upgrade-breaking hacks, just because someone decided to put a web site up called "no-www.org".
I agree with 'thelaw': this is something that should be repeated.
I also agree with 'thornelawler': this move seems immature, and I was completely surprised to see it come from WP after I've been continually impressed beyond all my expectations in every other area.
Finally, I'll say that I haven't contributed to WP in terms of code. So I guess I don't have any room to talk. But when something so controversial is brought up, I think feedback from the community is important, and I hope this comes off as constrictive criticism, because I didn't intend it to be a rant.
-Steve