On the issue of a UPS not being recommended, I guess that depends on the electric power quality you get and the level of risk you can take. I agree that's bad advice from Apple in general, specially when their warranty or applecare will not cover damages derived from electric power service incidents.
If your computer, the function it performs and the data it holds are too important to risk it with the quality of power you get, then by all means get a UPS. The type of UPS will depend - again, on the power quality - your power requirements and your budget.
First off, decide whether you need a true or a stepped sine wave UPS. SmartUPSs with true sine wave cost about twice as their stepped or simulated sine wave BackUPS counterparts, as they provide better protection and cleaner power to your computer. Also, some Mac Pro users found that stepped sine wave BackUPS couldn't handle the power surge the mac pro uses when starting up or waking from the battery, thus forcing them to switch to the more expensive SmartUPS, or to place a surge protector between the BackUPS and the computer - but this solution was not recommended by APC .
About the capacity or size of the UPS, I personally wouldn't go for anything under 1300 or 1500 VA - depending on the mac pro you have - for two reasons: a) you also need to consider the display plus any other device you'd need in the future... and b) most important, you must have a good extra margin for the intensity of CPU/GPU use you wish to cover plus the natural decline in capacity the battery will show as time goes by.
In my case, I got an APC Smart UPS 1500 for my 2009 2.66 Quad w/4 HD, 7GB RAM and the ATI 4870. It cost around $550 usd - a bit expensive, but it has been worth it: brownouts are common, and the power quality and service is not great here. The computer alone can run from battery for about 25 minutes under moderate use. By also plugging in 2x24" displays, the internet router, a powered USB hub, EyeTV250, desktop speakers, and 2 external hard drives, the whole setting will run off battery for about 3-5 minutes... enough time to give power a chance to come back, or to gracefully shut it down. Perhaps this SmartUPS 1500 was overkill, but as the battery naturally looses capacity with time, I will unplug non-critical devices and still have a nice margin with very low risk of harming my data due to bad power service.
Hope this helped. Cheers!