The DOJ is operating as if Obama is still POTUS. With Rosenstein in charge, this should surprise no one.
I believe the flaw in your logic is your assumption that Trump is afraid to fire anyone, let alone a supposedly insubordinate senior leader like an attorney general or deputy attorney general. There is just too much precedent to the contrary, including Trump's sacking of DAG Sally Yates for her refusal of the president's direct order. But it does not trouble me that others disagree, as time will tell what has really been going on for the past year.