In the usual course, the DoJ would pre-vet an E.O. and concerns about wisdom and justice, and particularly, as regards the former, issues of the degree to which defending the E.O. would require the DoJ to take positions that the DoJ has taken or would otherwise take defending other executive actions, and the potential adverse precedent (for public and even specifically executive branch interests) that would be set were courts to accept arguments the DoJ would make defending the E.O. would be addressed, weighed, and resolved (possibly with changes to the E.O. and/or changes to strategy in other pending cases) before the E.O. was issued.
The lack of consultation within the Executive Branch that, among others in other contexts, Senators McCain and Graham (both Republicans) called out, prevented that from occurring in advance, which meant those considerations would have to be weighed after-the -fact. But still before any defense could be prudently mounted.
"To the contrary, Yates claims she is ordering the Justice Department not to defend the executive order because it is not 'wise or just.' This is quite significant. I am not aware of any instance in which the Justice Department has refused to defend a presumptively lawful executive action on this basis."
Source: https://www.washingtonpost.com/news/volokh-conspiracy/wp/201...