Officials in Barr's office were briefed on the recommendations. It is not clear how much Justice Department officials pushed back, or why Shea signed onto the sentencing brief submitted by the career prosecutors.
Former prosecutors said the controversy further chipped away at the Justice Department's reputation for independence and will harm morale.
"The integrity of the Justice Department is now in question," said Steven Levin, a former federal prosecutor. "Federal prosecutors will admire the position that their peers took in stepping down from the case but they will be demoralized by the lack of integrity shown by the leadership."
Levin and other former federal prosecutors said they did not understand why the Justice Department didn't ask the judge for more time to craft its sentencing recommendation and continue internal deliberations.
"This is all extraordinarily embarrassing for the Justice Department," said James Trusty, a former top federal prosecutor.
Justice Department spokeswoman Kerri Kupec did not reply to emails or phone calls seeking comment.
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