The SCD has its quickest impact of the SI. It controls the bacteria there by cutting out their food supply. I was having a bit of trouble figuring out how it worked for the large intestine, since most of the food would be digested or fermented by bacteria by the time it reached the colon. Current reading suggests that the inflammation in the colon is at least partly due to one of the characterizing features of Crohn's - fat wrapping around the intestines. It seems that this fat is different from normal subcutaneous fat in that it consumes twice as much glucose as regular fat. One article said that by losing weight on a low glycemic index diet, you will selectively reduce the amount of this fat. The SCD plan is such a diet and so it would work (if it does work for you) by reducing the fat wrapping and the added inflammation that it produces. For more on the fat wrapping, see:
http://www.practicalgastro.com/pdf/June06/ArsenescuArticle.pdf