I take your point, but I'm not sure how hard they'll push that issue. My experience with several colleges of the University of London has been significant flexibility with the "ordinariily resident for three years" issue but great insistence on the "currently settled" bit. They likely won't go out of their way to investigate what precise visa she had on 1 Sept 2006, and even if they did, it's just the matter of one month.
This is a matter of the registrar's discretion, though. My experience is that they really care about the ILR issue. Your mileage, of course, may vary.
And to be honest, I'm not sure about this statement entirely:
As a visitor, you were not lawfully residing in the UK on September 1st 2006, so you were not ordinarily resident.
The definition of "lawfully residing" may be left open to interpretation, particularly considering that it was quickly followed up by a spousal visa. She was definitely "lawfully present". Whether or not, given the context, that may be extended to residing, I don't know. But again, from my own personal experience, I would anticipate a positive result.