The result is desirable for neither side. Neary is probably right when, judging from previous attempts to develop shells for GNOME, he suggests that "Canonical's management has seriously underestimated the difficulty of the task in front of them."
In other words, the development of Unity may be more than Canonical and Ubuntu alone can handle -- yet the ongoing dispute means that few allies are available.
In fact, not even the whole of the Ubuntu sub-community supports Unity: the change is largely irrelevant to Kubuntu and Xubuntu, which rely on different desktop environments, while Edubuntu intends to support Unity as "an optional installation rather than a default," relying on the existing version of GNOME as better suited for its technical purpose and because it "currently offers better usability."
Similarly, mainstream GNOME also suffers from the division. One percent of software improvements may sound low, but in a project as long as GNOME, that is still 4,487 commits.
More importantly, according to Sergey Udaltsov's blog, in the past Ubuntu has always been a major source of feedback to GNOME development. He worries that the lack of Ubuntu feedback might adversely affect the quality of GNOME 3.
Although commenters on the blog were quick to dismiss Udaltsov's concern, it is a rare free software project that can afford to turn away any contributions. By sheer weight of numbers, GNOME can probably survive the lack of Ubuntu's support better than Ubuntu can survive the lack of GNOME's support, yet the point remains that any loss of support affects a project.
In the end, the right or wrong of Unity's place in Ubuntu hardly seems to matter compared to the very real possibility of yet another permanent division in free software. Yet, while in an ideal universe, both sides would realize that their differences only benefit their proprietary rivals, in this one there seems little chance of that ever happening.