-It sounds like the water filter is a "must" have. The piece of mind it affords you is worth the extra few ounces.
If there is plenty of anything along the CT, it is water! The longest stretches *on trail* without are from Sargents Mesa (Tank 7 creek, 12 miles into segment 16) to Lujan Creek (20ish miles into Segment 17). And then from near Spring Creek Pass to beyond Carson Saddle. While it's not actually that far, these are long and difficult miles. In 2009, I rode with only 3 water bottles, and I was pretty thirsty through there, especially after a bivy.
I did not take a water filter, but I had a gnarly case of Giarda when I hit Durango. IMO, it's a tough call. So many of the water sources are high enough to be completely clean, but it only takes one bottle downstream of a big cow pie to cause some serious damage. I've always felt that a filter was king because of the speed and ease at which you can get clean water, but I think a Steri-Pen would be a fantastic alternative. Super light, and you only need to use it on questionable sources. Tablets are even lighter, but ya gotta wait...
Good luck in 2012!