I would have to disagree, almost every pro I know lets the camera do at least some processing of the images. I just wouldn't set the sharpening to high. Normal works great.
If I was going for the NTH degree of image quality then I'd shoot RAW and spend hours in front of the computer working with the image.
BTW, I had a deposit on one of the first S2's but when I saw the crappy color results people were getting at the time I opted for the D100. It took awhile for folks to figure out how to get the best color out of the S2's and now what I see is very, very good but I still like the skin tones out of the D100 better. It's a matter of personal taste. (too often the Caucasian skin tones still look too coral colored with the Fuji for my taste.) (Granted, the Nikon skin tones can come out too orange sometimes) (My old Canon had trouble with reds coming out too magenta looking) Every camera has it's own pecularities. Another thing I liked about the Nikon was it's battery. That thing is GREAT! The Fuji has Firewire which is great if you're teathered to a computer, like in a portrait studio. One little test to perform, go to your camera store and hold the cameras vertically, viewfinder to viewfinder and quickly look back and forth between the two. See which looks better to you. Resolution wise they are still both native 6mp cameras, the Fuji does some resampling to get it's higher numbers. Check out Thom Hogan's site, he literally wrote the book on the two cameras. He's good at pointing out their strengths and weaknesses.
Good luck on your decision! Don't forget, the glass you use is VERY important too.
My two cents worth.