If MS feels threatened by Mono, it changes its runtime and kills interoperability. From that point on, Mono is playing catch-up and who knows what happens to the users caught in the middle.
Even if they had some magical changes that kills interop (like, what, I don't know), Mono still works with all current apps at that point, and only developers adopting the new, not-compatible system (and thus discarding all their old libraries) would be affected.
Microsoft sorta has done this, with Silverlight and WinRT. They required different stdlibs and a bit of runtime tweaking, as I understand. Silverlight was handled by Mono, and WinRT - not sure if anyone is interested, as it's really for Windows Metro applications.
There are enough people (especially enterprises, their most important customers) using .NET now that Microsoft has to be very careful about any changes they do make to avoid breaking existing applications and upsetting their paying customers.