Not a big deal for Mono
I don't think it will affect Mono much, because Mono never had any success outside of a few niche markets (primarily games). Mono has been around for years, but it was met with a big yawn in desktop and server markets on Linux, BSD, and Mac. Java developers weren't interested in switching, and neither was anyone else. The few Mono applications which were written were demos intended to show that Mono worked.
Nothing of any significance was ported from Windows to Linux because DotNet was never really a portable system. There are too many Windows assumptions baked into it, so making a program cross platform using Mono was in reality a port, just like writing it in C++ would have been. Software vendors who wrote stuff in C# weren't interested in being cross platform, and developers who wanted to be cross platform generally picked something else.
Some people happen to like C# better than Java (and visa versa), but quite frankly the rest of the software world just saw C# as Microsoft Java, and if they wanted Java they would just use the real thing. The value that C# and DotNet had was better Windows integration. If your platform wasn't Windows, then that advantage disappeared and what was left wasn't really all that compelling.
When Novell was bought out by Attachmate, Mono was dropped like a hot potato. This is why Xamarin was formed by the newly redundant Mono developers to focus on the mobile market. Their value-add isn't Mono though, it's all the extra bits and services they add onto it. They could have used anything as their core run time and got the same result.
Unless Microsoft is going to duplicate all of Xamarin's work to compete directly with them (which I admit they could), then it makes no difference whether Xaimarin ship Mono or Microsoft's run time. I should correct that - the Mono that exists today is oriented to the mobile market. What Microsoft actually open sources might be too bloated or otherwise unsuited to mobile, as de Icaza mentions in the interview.
Five years from now it might be a different story, but for now, I expect Xamarin to cherry-pick a few bits that they like, but otherwise nothing will really change.