How many times have we seen companies that can't compete with their substance turn to advertising, public relations, and, as a last resort, lawsuits, to protect their interests? If Microsoft has to take that road, what does it say about the company's ability to provide true security, or its ability to innovate? Nothing good, certainly.
At the same time, Microsoft's PR blitz will bring the concept of open source software before people who may never have heard of it before. Raising it as a competitor legitimizes it for big corporate organizations.
Microsoft's arguments should be easy to refute. However, while Microsoft will be spending beaucoup bucks to get its message out, the open source community doesn't have that kind of money to spread around. It's possible that Microsoft could win a PR battle with misinformation and a big checkbook.
Against that possibility we have power of a free press, which likes to take a contrarian view and look at the facts objectively. And we have the real-world experience of administrators who have handled security issues in both Windows and open source software. It will be up to them to speak to their peers, their managers, and the media to get out the truth and fight the propaganda.