Yes you could say ' where' as well as ' whereby' . The word ' whereby' is used for saying that something is done according to the method, arrangement, rule etc that has been referred to previously. Your sentence can be rewritten this way: You think that your department should go to an "open office" design which will involve taking out all the cubicles.

"Whereby" can be used instead of saying "by means of" or "through which". So in this sentence, it means that the new "open office" design is achieved by taking all the cubicles out. (the design is made by means of removing cubicles). Hope this helps!