I believe you are being overly harsh about the CD staff. In fact, the court explicitly said that they would treat the lower court's ruling as, and apply the standards applicable to, a preliminary injunction, even though it was, technically, a temporary restraining order. I'd cut lay readers a little slack here.
I do recommend reading the actual order here..
As for the future proceedings, the government may appeal to an En Banc hearing before the Ninth Circuit, appeal to the Supreme Court or allow the case to return to District Court. A smart President would likely allow the case to return to District Court, because his chances at the Supreme Court might be limited, given the possible 4-4 split and the likelihood that the Supreme Court would rather wait for the case to come before it in a more finalized position (after the merits have been litigated). This would also increase the chances it would be a nine member court that would hear the case.
On the other hand, we have an egotistical, maniacal nut-case for a President who is unlikely to exhibit that level of constraint, so I wouldn't be surprised to see him go immediately to the Supreme Court, where he is likely to lose again and, at least in the short-run, lose more political capital.