Lyle Denniston at SCOTUSblog is sympathetic to the original ruling which the 9th Circuit has now "erased", but he must concede that it's decision couldn't be more final:

One of the modern gay rights movement’s most significant courtroom victories — a California judge’s ruling last year striking down the military’s ban on gays and lesbians — is about to vanish from the federal record books, as if it had never happened. It will do so because the Ninth Circuit Court refused on Wednesday to reconsider a ruling that erased the decision, and everything about it, and barred any gay rights lawyer from ever trying to use it to help in any other case. The brief order by the Circuit Court, denying rehearing by a three-judge panel, also noted that no judge eligible to vote even called for a tally on reconsideration by the full en banc court. This was a final legal victory for the Obama Administration in a case that at times had been bitterly contested.

... The denial of further review by the panel and by the full Circuit Court also left intact a blistering critique by one of the three judges of any jurist who would use a 2003 gay rights ruling by the Supreme Court — Lawrence v. Texas — as the basis for recognizing new rights for homosexuals.

... The panel said: “We vacate the district court’s judgment, injunction, opinions, orders, and factual findings — indeed, all of its past rulings — to clear the path for any future litigation. Those now-void legal rulings and factual findings have no precedential, preclusive, or binding effect.”