6D RAW support is only available with Aperture 3.4 or later.
Please confirm which version of Aperture you are using?
When you say they look darker, what do they look darker than? (do you mean they look darker than the image on the camera, or something else?)
The camera will save two files - a JPEG file and a RAW file.
It is normal for RAW images to appear slightly darker than JPEG images.
The file you are viewing on the camera is the JPEG file, so you will not see the true RAW image until you download it to the computer.
Let me know if the firmware update improves this for you.
Ok, a future firmware update should do the trick!