This is an excellent point. Now Apple is forcing their customers to get whole new desktops instead of upgrading them (that statement nauseates me to type), even though I'm sure most professionals (ESPECIALLY the ones I'm with) would much rather just have custom built windows workstations, or worst case, have to build a hackintosh.
I think you're misreading the Mac Pro's intended audience. It's not aimed primarily at IT workers, but at photographers, graphic designers, movie editors, and other professionals in the creative arts. How many of these people want to build their own system or spend time monkeying around with an upgrade to the video card? Most professional workstations are bought off-the-shelf and not substantially updated throughout the life of the equipment.