I think the Quadro FX 5800 is very likely since the Mac Pro is missing a high-end GPU option. The 512MB HD4870 is a mid-range card with a MSRP of $150 so it should have replaced the HD2600XT not the 8800GT. Personally, I'm hoping that Apple adds the upcoming 1GB HD4890 alongside the Quadro FX 5800 since the HD4890 is a true high-end GPU.
You may feel the 4870 is a midrange card but it is not. It is at the low end of AMD's highest consumer tier and the basis of their high end pro cards. As for replacing the 2600XT, price isn't as relevent as it being noisey and you couldn't fit 4 in a Mac Pro.
The delay with the Quadro FX 5800 probably isn't engineering resources on Apple's part but more availability of the 55nm GT200b chips since I'm guessing nVidia is concentrating them on the desktop market to beat back ATI's HD48xx series.
The FX 5800 uses the older chip found in the GTX 280 and I can't see them forgoing selling a $3000 card to Apple for the AMD battle.
The following is based on what I have read and been told:
Apple develop the drivers themselves for Nvidia cards and driver development for the previous Quadros probably wasn't too hard or much of an issue as they also were selling GeForce cards that were based on the same hardware. This time they don't have a GeForce card to share that development with, so they would be developing drivers soley for the Quadro. I can easily see it just not being worth them doing it due to sales volume. I don't know how much effort is needed for such things, but I assume it isn't trivial given Apple's very limited set of cards.
In regards the 3.2GHz model, if it's introduced it'll have to be as an option on top rather than directly replacing a previous model since Intel has no near-term Xeon price drops planned. People shouldn't have much reason to complain since there would be no changes to existing configurations.
Agreed, I'm certainly not going to be suprised if they turn up from Apple.