I have the Defender case and I absolutely love it. I personally haven't had any trouble with the screen. The pen works fine and although if I look hard enough I can see where the screen is slightly raised off the phone it has never caused any problems.
My phone gets shoved in and out of my pants pocket, coat pocket and my purse and the case has kept it in perfect condition.
Looking at it I would say if you wanted to take the screen protector off it doesn't seem to hard to do. It looks like it's just glued around the edges of the screen to the plastic. worse case I would just cut it off and use a new protector.