I estimate if 2 x X5650 is not overclocked it will get about 275 fps. The L5640 is rated as 2.26Ghz and 2.79 Ghz Turbo. I think it is showing a decrease in 2x hyperthreading is because the system can not supply 24 threads with enough data. Even with 12 threads the system can not keep the cores at 100%. Also, if 2 threads are running in one core and it is just waiting for data then it will just slow down that one core.
I ran Cinebench 11.5 without Hyperthreading and it shows 12C/12T @ 2.27GHz, Intel Xeon CPU L5640 = 9.56. With Hyperthreading it shows 12C/24T @ 2.27GHz, Intel Xeon CPU L5640 = 11.59.
If I am not using the HD 7750 my system maxes at at about 250 watts. At idle about 135 watts. Anyway all I got in there is just 1 hard drive, 1 sound card, 1 HD7750 gpu, 2 x L5640, 6 x 2Gb DDR3 1333. Remember L5640 is rated at 60 watts and X5650 is 95 watts. If you want the test I used for Handbrake go to this thread: There you can see a single L5639 overclocked to 3.8 GHz get 240fps. A single i7-4930K @ 3.40GHz get 317 fps. Maybe you are better off with the new cpus.
http://forums.anandtech.com/showthread.php?t=2327881