This increased CPU usage wasn't coming from having to drive the 2560 x 1440 resolution from a composited desktop as when using a 2560 x 1600 Samsung 30-inch LCD display over dual-link DVI there isn't these problems. Disconnecting the USB and Ethernet piggybacking on the display's Thunderbolt connection also didn't alleviate these load issues. The load was dragging down the system's usability, not to mention also causing the CPU to burn through much more power than needed since it wasn't dropping to a lower power state.
When connecting the Retina MacBook Pro to the Thunderbolt Display with Ubuntu Linux, there was the same Thunderbolt load problems again that even the Ivy Bridge system would basically be useless for a Linux desktop with the beautiful but demanding display. This increase load was coming from the kernel -- it appears from within ACPI, but I'm not positive. I've tried different kernel command-line boot options as well as the latest Git code to no avail. When booting either system to OS X instead, the CPU usage while idling at the desktop is zeroed out and there are no problems.
The investigation into the Thunderbolt Linux situation is still ongoing and will be updated accordingly. So the display can work under Linux as well as the connected devices running off Thunderbolt, but the current high CPU usage renders it nearly useless. Another issue will be without any on-screen display or menu controls, backlight adjustments might be a problem under Linux (in OS X they are exposed in software). Due to the Linux problems, plus some Retina MacBook Pro shortcomings when using Ubuntu Linux -- to be detailed in a later Phoronix article -- that system is now having to run Ubuntu Linux atop OS X with VMware virtualization in order to take advantage of all available hardware features without severe limitations. If you don't mind spending $1000 USD on a monitor and are interested in Thunderbolt technology, the Apple Thunderbolt Display is great, but not yet a device I would call Linux friendly and recommend holding off on purchasing the Apple hardware until all issues are worked out. OS X 10.8 vs. Linux benchmarks are also forthcoming.