Ok, maybe you're tensing, while not enjoying the noise, which is causing the headaches? I've got issues with high pitched sounds, too, but they have to really pack some decibels to give me headaches. I have additional problems with my ears (eustachian tubes), which combined with allergies make for some sinus headaches to rival migraines, but not from something like cherry blues. Even a loud club, where I can hear ringing later, won't necessarily give me a headache. You really need to isolate the keyboard as a variable, before chalking it up to the keyboard though. It is possible, you're getting headaches, from other factors occurring during your computer usage. You are consulting trained medical folks, I hope.
That said if you don't like the sound your board makes, sounds like you should try to swap for browns, but if you really want quiet, you're gonna have to go Topre. Browns are not quiet, even when you don't bottom out. Additionally, PCB browns are quieter than plate mounted browns.