Is it a bad idea to change/remove a co-author from a manuscript which is revision?
You need documentation that this person doesn't believe that their contributions merit co-authorship (or that they didn't contribute at all). I would write them an email like this (adjust as necessary for specifics and to not upset them further):


  Dear Charles,
  
  Last Monday you mentioned that you do not want to be listed as author
  on our paper "The missing link between dinos and birds" since you believe your contributions to be too minor. I just want
  to make sure that we are on the same page: Can you confirm that you
  would like me to remove your name from the author list?
  
  Thank you, 
  
  A. G. Install Happyness


If they confirm, you are free to tell the editor that the co-author was included by mistake and agrees to be removed from the manuscript. If they don't confirm you need to clarify what outcome they desire and then discuss this with them and the other co-authors.