The cause of the stress on the wrist for most people seems to be the same as in my case: clicking the mouse. While excessive keyboard use can also cause issues, the problem often begins with mouse-clicking. It follows that if we could play RTS games without clicking the mouse, the risk of carpal tunnel would be greatly reduced for most of us, even when playing extensively.
You can test this out by playing some more casual PC games where you control the game camera using the mouse. Many of these games allow you to remap the mouse buttons to certain keys, such that you only need to move the mouse and never need to click it. This got me thinking of how to achieve something similar in RTS games like StarCraft. Unfortunately, I do not believe that any of Blizzard's RTS games allow you to do this. That's where AutoHotkey comes in.
AutoHotkey can be downloaded here. Once you have it installed, open Notepad, paste in the following code, then save the file with the extension .ahk.
+ Show Spoiler +
*Capslock::
MouseClick, right,,, 1, 0, D
KeyWait, Capslock
Send {Capslock Up}
MouseClick, right,,, 1, 0, U
return
*Space::
MouseClick, left,,, 1, 0, D
KeyWait, Space
Send {Space Up}
MouseClick, left,,, 1, 0, U
return
^!s::Suspend ; Ctrl+Alt+S
After running the file, CapsLock will be mapped to right-click and the Space key will be mapped to left-click. Use Ctrl+Alt+S to toggle this functionality off and on.
Now you can drag-select by holding Space, moving the mouse, and then releasing Space. Moving groups of units becomes 1-CapsLock, 2-CapsLock, etc, and attack-moving becomes 1-a-Space, 2-a-Space, etc. This will feel very weird at first, but stick to it and you will develop muscle memory for it. Since you probably will not want to jump into competitive play, playing through some campaigns using these controls would be a good way to get used to them. Eventually, they should become second nature. I feel pretty confident that with enough practice one would be able to play at a high level using this control scheme, but I cannot attest to that since I never played at a very high level.
Hopefully this will help at least one person. It has certainly helped me relive my love for RTS games.