i have really sensitive eyes!! i keep my computer at the lowest brightness most of the time, and have a colour filter too.
i usually turn up the brightness a notch or two and turn off the filter when im doing colour work, but this isnt really necessary if you have a pre-set palette - at that point, its more or less painting by numbers. you could also, instead of keeping the brightness up all the time, pop it up now and then to check everythings in order?
how bright do you have it, anyway? imo you can afford to go pretty dark on your screen, because thats how a lot of your readers are gonna be viewing it (especially on mobile - who the hell turns their brightness above the middle mark on their phone?). it could also help to get yourself f.lux - a colour filter app that filters out blue light on your screen, which is probably whats making your eyes hurt. if you keep that on a really strong setting for the rest of the time, alongside taking breaks when your brightness is up, you should get enough eye-rest to avoid massive headaches.