First, Samsung did exactly what Google suggested to Cornerstone / CyanogenMod - make it an optional extension that apps can opt into. Here's some (unofficial) documentation about that: http://www.modaco.com/page/news/_/android/developers-add-sup...
Second, I have a Galaxy Note 2. Applications that support multi-window on my phone (i.e. where the application developer has opted into the feature) include: Gmail, Chrome, (Google) Maps, YouTube and (Google) talk. I'm sure all of that was done over the vociferous objections of Dianne Hackborn and the rest of the Android team.
There is a risk to Google that if there is not sufficient diversification in the Android market then Samsung can do what they want - including in an extreme scenario forking away from stock Android and creating their own lock in ecosystem to go up against Apple. (this is an extreme scenario - but I don't think its impossible)
Remember non-tech savvy people may just enter a store and think do I want an Apple or Samsung phone/tablet.
I also wonder if the real purpose of the Nexus devices are to help get other devices makers up to speed to compete with Samsung.
If the perception that "Android is a battery hog" because of widgets and having a more "real" multi-tasking system, hasn't negatively impacted Android yet, this certainly will. At most Android tablets just need a split-screen view.
Microsoft is at least heading in the right direction since Windows 8 allows two programs metro apps to run side-by-side. Unfortunately, even their implementation has flaws: it only allows fixed sizes of 70%/30% or 30%/70%. Users can't manually adjust the divider between the apps to 50%/50%.
