THe DOJ is part of the executive branch, (the attorney general is a presidential appiontee), so it's no surprise that the DOJ takes its marching orders from the administration, which, in this case, happens to be republican. Look back in history and you'll see that this has always been the case.
Dems and Reps have both played shinanigans with our civil liberties. One of the worst offenders in this regard was FDR; a democrat, who ordered the internment of 110,000 Japanese Americans, citizens included, among many other things.