The silent DNG appears to have more noise than the small CR2 (but without you supplying a full size CR2, there's no OB areas to get an exact amount). This makes sense. The silent DNG came from video mode where resolution is reduced by line skipping, while the small CR2 likely benefited from proper downsampling (when downsampling resolution, neighboring pixels sort of get merged together in a sense, which has the effect of reducing noise, in other words there is a trade off between noise and resolution that we are taking advantage of).
There are additional reasons silent DNGs would have more noise: the sensor is in a different mode where it is continuously read out, this causes the sensor to heat up and the heat increases noise (there may also be other effects on noise from this mode besides just heat, IDK).
If you want a more fair comparison, use crop mode for the silent DNG, and compare it to a full size CR2.
You can compare the noise yourself in camera using raw_diag (from here:
http://www.magiclantern.fm/forum/index.php?topic=10111.0).
If you need to capture more DR then: ETTR properly, use dual ISO (should work with silent pics, but you might have to be in movie mode), and/or consider actually using your shutter.