I have the same exact probem, have gone through all the unibody MBPs (15" and 17") with similar results on all of them (headaches after only 20 minutes of use), I keep returning each one after giving them a fair shot. Before using any unibody MBP i've been a solid MBP user and have always loved the screens and never had a problem with them. I use computers for about 6-8 hours a day, and typically use my old rusty but solid 2007 Macbook pro (non LED) for about that long straight through, no problem.
Heres where I stand, hopefully this helps anyone else who has this problem.
1) I used to think it was a problem with LED, but now I realize its not LED per se, its the way the way the MBP screen is built/designed/wide gamut/whatever. I say this because i've since purchased two generations of MB Airs which use LED and love the screens, no headaches what so ever.
2) I decided to keep my most recent 15" MBP purchase just to keep as a backup, and ran a Spyder 3 elite (color calibration) on it, and to my surprise, it actually helped with the headache situation ALOT! I still get headaches from the screen, but now instead of a headache after 20 minutes, I can go for about an hour before the screen starts to hurt. Spyder3 visibly took the edge off the artificially high contrast colors such as reds and blues, so I think the headache issue might be related to the color gamut of these unibody screens, but thats just a guess.
3) The only real solution to this issue if you want to use a macbook pro is to connect it up to a high quality external monitor. Thats what I use now, its not ideal, but I dont think apple will ever address this issue that whatever small minority of us have with headaches, so if you want to keep using apple products, this is the only real solution