Perhaps post the original CR2 file so someone can check it out with their setup. The main difference I see in the posted jpegs is that the lightroom image is much brighter, inndicating that settings are different between the two.
Anyone who says that images taken at high ISO's are noise free probably have a huge tolerance for noise. Noise is noticible with no NR starting at ISO 800, but the main thing is that it does not increase wildly at 12800 or 25600 like it did in the 5D MK II. I find that starting with ISO 3200, NR is always required, at 1600 or 800, it might be required depending on the colors in the scene. Blues are the most difficult.
I put up with high ISO noise, because it doesn't show in prints (fine detail is lost), and because I have no other choice in extreme low light.
When using RAW, some NR is needed at high ISO, and at 12800, a ton of NR is needed!!
Also note that DR is very thin at high ISO's, so even with perfect exposures, you need to make adjustments.