The US government isn't unitary. The executive branch controls enforcement policy, the judicial branch controls interpretation, and those can disagree. Your “they” refers to separate institutions that do not have control over each other.
He's implicitly saying that the legislative branch is failing here, so yeah, it's bad overall. Plus the executive branch does have significant control over legislation, and it's also bad that they're not trying to fix the law.
Overall, this individual move by the justice department is good, but it's bad that more isn't being done.
