All risk analysts know that senior management in an organization are, by sitting atop the chain of command/accountability, able to selectively disapply, countermand, or subvert systems of control, if they are motivated to do so.
Where multiple senior personnel (including those within an organization, and outside it - the DOJ in this case - that should have been a failsafe check on the FBI) collude in such endeavors, no system of checks and balances can function.
The seriousness of what occurred cannot be overstated. The threats to national security of a similar derogation of established protocols in/between other departments and agencies should be easy for the fertile minds here to envision.