Why would Apple want to kill this?

MonoTouch is not significantly different from Unity 3D, which has been used to create over 40 games for iPhone already.

The primary difference is, instead of needing to create user interfaces purely atop GL, you can use the CocoaTouch libraries and get native buttons, frames, html controls, etc.

Microsoft did rebuild Windows from the ground up as a modern operating system. That was Windows NT (as compared with Windows 3.0) back in 1993. Thus, they predated the "let's rebuild the OS from scratch" thing that Apple did by 8 years.

That said, even as a modern operating system, it has a number of anachronisms kept primarily for backward compatibility with legacy 16-bit code, and has even more backward compatibility "hacks" for poorly written 32-bit apps (see the oldnewthing archives -- lots of apps do stupid things), but their priority is keeping existing code working, instead of breaking existing (poorly written) apps. I can't fault them for this.

The only thing removing such anachronisms would do is prevent older programs from working, which really does no one any good (unless you like the thought of Microsoft shooting their own lower-torso off...)