Like most things Microsoft, this is a matter of being able to leverage something for all its worth. Skype is no different from any other acquisition that has since become part of their greater company portfolio. This an opportunity to further Microsoft's patent roster. They made forays into the market with Web search, why not see how it goes with VoIP?
For Microsoft, voice and video communication solutions is an area in which Google doesnt already have a dominant lead. Bundle this with the benefit of adding Skype to their enterprise offerings, and I can see why Microsoft decided to drop an awesome sum on this communications technology.
Regardless of how all of this plays out, at least we've seen evidence that Skype's new direction won't really have much effect on the destiny of the Linux desktop.
Missing Skype won't stop desktop Linux
As big of a pain as Skype's failure to develop at a reasonable pace has been, it hasn't affected Linux adoption at all. Despite Microsoft's belief that Skype is a "win" for them, the truth is that existing VoIP solutions for the enterprise already fill needs for today's business community. As for home users, we're already using mobile phones. Skype really matters very little to anyone, with the exception of video chat. It's becoming increasingly clear that the only thing that really adds value to Skype at all is video chat and Google has already made significant inroads there.
If Google could hurry up and release a native Linux version of Gtalk with video chat, concerns over the future of Skype for Linux will disappear almost overnight. But until this happens, we'll be left with a mixed bag of Ekiga, various chat clients and of course, Google Chat via Gmail. Far from a clean-cut sort of solution, but it's still better than nothing for the time being.