Let me preface this piece of thought by saying that, yes, a new team leadership has every right to want to choose the people who work in their system. My suggestion, though, is that they not make removing the current and first-year Vice-President of Player Personnel David Bell part of the coming changes to the organization.
The San Francisco Giants do have a lot to fix in their system. There may be organizational flaws in thinking and in practice. A teardown o the organization Brian Sabean built and led for 20 years would be controversial, but easily defensible.