How is it making him a scape goat if the charges issued are valid, relevant, and rational? As I said, the guy does not need to be booked for murder or manslaughter to force a systemic change with the behavior of law enforcement. A simple statement from the Grand Jury that "charges will be allowed for excessive force" would suffice.
If as you say the department(s) are at fault this will come out investigation for the use of excessive force. Legally, it would most likely result in the charges being dropped for the officer and the attention being diverted to the department. Where it should be also, but we can't seem to tackle numerous problems simultaneously during a legal process.
In reality, this is making the department the scape goat for the officers actions and not the other way around. Unfortunately this is the way it has to work due to legal precedent. If the departments training changes and future issues occur, then individuals can, and should, be held accountable for their actions.
Complacency I'm sure you will agree will result in zero change.