What does it mean to be dead then?
What I think Paul Graham is saying, and this is underscored by the notion of "being dangerous," is that Microsoft is no longer the place where new ideas and true innovation is going to come from. Startups are born from fresh ideas, and the companies that are dangerous to them are places like Google which seem to being designed to produce competitors to startups.
Microsoft will continue to sell $50 OEM copies of Windows to Dell and licenses of Office but this is a business on the decline. Microsoft is Old-tech stuck in the era of desktop applications, closed development strategies, and the economics of software licensing.
The financial effects of MS being dead are already showing some effect, MSFT has moved much since the dot-com boom, but it will take 5-10 years and continued blunders from MS to see some real damage.