If Microsoft manages to go an extended period of time without hackers finding oodles of vulnerabilities, then I'd consider them for mission-critical military systems. We may be more similar than you think. We are mostly a M$ shop now (with a history of VMS, Unix, Apple, Novell) but still have some critical Unix systems. Unix still has a place. I just don't support replacing it with Linux.
DoS is one thing. Actually penetrating system security to run malware and/or access information on the network is something else.
It's not that far of a reach at all. It's all crime, closely related by technology.
I can go along with the UNIX/Linux divide many dont see, there are some scalability issues with Linux (not many mind you and its nothing that cant be bodged together) but for a large DB server I am going to go with SUN. For a web load balancer I am going to go with Apache on Linux..