There's nothing wrong with Roman Harper. Do you see how good this defense is playing without him? We've seen this move before. This is the same move that Payton used when he benched Joe Horn for the younger talent at wide receiver. What you are seeing is Payton being very "classy" in showing Roman Harper the door.
After all, would this (the #11 ranked defense in the NFL) be any better with Harper on the field. I submit to you that you won't see Harper again this year. Our safeties are Kenny Vaccaro, Malcolm Jenkins, Rafael Bush, and Isa Abdul-Quddus. Keeping Harper on the roster, but inactive every week, allows him to share in whatever hardware the team may earn for this year, and that's what makes this approach so "classy".