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.
Microsoft may not get a "controlling stake", but it will probably have a huge influence in the development of Cyanogen from now on.