By your description it seems that there are processes and not just libraries that GNOME2 applications can depend on, such as gnome-panel, that aren't parallel installable with GNOME3. I'm not familiar with the internals of GNOME but what about notifications or IPC or VFS plugins?
It seems that it would be good to make the same sort of platform API guarantees that the Linux kernel makes to userspace or that glibc makes so that third parties can expect their application binaries to continue to function for decades and that the system won't be deprecated out from underneath them.
Anyway the main point of the article is supporting a GNOME 2 style theming using extensions to GNOME Shell which seems like a good idea for users who prefer the old style workflow. Even Windows maintained a classic interface option when introducing changes XP and 8 and was more successful for doing so. This is a positive thing.