I use a tablet myself sometimes, but I'm not sure how good of a substitute it would be for a mouse... I suppose if you use it for a while though you can probably get use to the change, and if you are already experiencing carpal tunnel syndrome then you probably have no choice but to give it a try. Those trackball / roller-ball mice may be another option worth trying as well.
You could also try getting a program like dragon naturally speaking, or another voice-to-text program, and substituting that for your typing and that may help a bit. I tried it a while back and the technology has really come around in the last several years.
My biggest advice though, as in piano playing, would be to continuously take breaks when you feel fatigued. NEVER work through pain as that is only compounding the problem and making it so you have to work through more pain the next time.
Since you play the piano as well, if you opt to continue using a keyboard, type like you would play the piano and lift and relax your hands after sentences as you would at the end of the phrase. On that note make sure it is not your piano technique that is the cause of your hand pains.
Jam it back in, in the dark.