I've had a lot of nvidia cards fail on me, over the years. ATI/AMD? Never once. All things being equal, I'll always prefer AMD.
That said, this whole article is a bit silly. Sure, nvidia might be the default choice in many or all of the standard configurations, but there will be AMD cards in the mix for custom orders. I would be surprised if the majority of Mac Pro orders were not custom built as it is, so who really cares? Hopefully whatever the top end upgrade is, it's a very, very nice card.
The suggestion that Apple will wait for workstation Ivy Bridge chips is also ridiculous. Of course they won't. The only reason Apple has waited so long to release a new Mac Pro is because Intel hasn't made a suitable chip yet. Soon, they will, Apple will use it to upgrade the line, and life will move on. Hopefully, Ivy Bridge workstation chips won't take years to come out, and Apple will be able to upgrade the line again sooner.