I think it's a valid reason.
It's a valid reason for you not to enjoy watching a movie. It's not a valid reason for the commercial film industry to back away from 3D when they have every good economic reason to move in that direction.
Why should I be forced to feel discomfort and pain just to watch a movie?
No one's forcing you. You can wait to see a movie - assuming it interests you - in some other format.
If headaches, etc affect a significant percentage of the theater-going audience to the degree that they don't pony up for tickets, it will be in the studios' best interests to correct that problem with the glasses.