The Scouting Dept. has nothing to do with letting players go to other teams. That is mostly on the HC and to a lesser extent, the GM. The HC decides who makes his football team unless the GM tells him he has to keep a certain player(s). Yes, the Bills' Scouting Dept. should get kudos for recognizing his talent. It would be mostly the fault of the Bills CS for not developing him, and GM for getting rid of him instead of the CS.
No, the scouting dept. doesn't determine what system a team uses. Sometimes they try to project a player being able to make the transition from one system to another and miss. At other times they try to force a player who has a very definite set of skills, then take him "hoping" he'll fit a different system for which his skills and talent really aren't suited (square peg into round hole). Then and only then should the Scouting Dept. be blamed imo.