I think Beacon is a lot like the news/mini feeds. Both were radical ideas that faced heavy privacy opposition. Facebook rode out the wave once and seemed to be planning to do it again, but I think they miscalculated on one thing: since Beacon is openly commercial, Facebook looks more evil than misguided. I think there's a new idea behind Beacon that is plainly good: aggregating stuff about your friends that's happening in the general internet. (Paul Buchheit's new company is doing this.) The right move would have been to release that function with no commercial facet, and work that in later when this idea is no longer new.
What's in it for Microsoft? I'm guessing Facebook is an important part of their online advertising plan, and they are going to get preferential treatment and power in excess of their share.
At least thats how it might play out, the root cause could still well be Zuckerberg's arrogance.