This is a very minor investment, and won't give MS any sort of controlling stake. It's very likely that they want to use this to keep a better feel for the pulse of the direction the Android ecosystem is going in than any sort of power play or to adapt technologies.
If we won't see Microsoft apps and services start popping up in Cyanogen 6 months from now, then I'd agree with you, but I think that's exactly what's going to happen.
Microsoft may not get a "controlling stake", but it will probably have a huge influence in the development of Cyanogen from now on.
Microsoft already publishes heaps of android apps[1], but there's no way Cyanogen would drop Google apps (leaving ASOP) to pre-install a suite of unrelated, relatively useless apps (drop Maps, gain Office Suite?)
I think the whole Cyanogen thing is that they make these services optional. If this means Cortana can be an optional service in CM (and not to the exclusion of others), I see zero downside.
