I don't know about noise performance, but it would be a big plus for the camera to share compact flash with your S2. If you used AA batteries already, then the 5050 is a great choice since you would get away with no new media or batteries. Since you use the DS-125's, you may not use rechargable AA's at all.
On my upcoming trip I desire the ability to use CF, a panoramic tripod head, and cold weather batteries. The Nikon 5000 seems best for that application. The point is that you may want to consider a variety of potential uses.
I personally like to leave my SLR in the housing at all times, so any topside photography is always done with another camera. Maybe you should just get another S2!