Well, the Prime Minister and the Department of Justice did exactly what I hoped they wouldn't. They appealed the court order requesting the repatriation of Omar Khadr. They have also applied for a stay of the order of the Federal Court of Canada so they would not have to ask for Khadr's return before the Supreme Court of Canada has decided to review and either accept or not accept the case. If the Supreme Court does not accept the governments appeal, then the Federal Court ruling stands. This is slightly odd because most legal proceedings are put on hold by lower courts once they realize the Supreme Court might look at it and say something, but not always. One of the governments arguments may be that there are still ongoing legal procedures in the U.S. against Khadr, however, this may be a misnomer as most of the procedures have been suspended pending further legal review. At this point, that technically means the U.S. government doesn't know how to prosecute him.
With that said, the Canadian government could definitely ask for Khadr's repatriation given the U.S. government isn't doing very much with him at the moment other than housing him. Repatriation does not mean release. It just means basically moving a citizen from whichever country they are in back to their own country. I can think of one major reason why the government doesn't want him back. As soon as he arrives in this country, he all the protection of the Charter of Rights and Freedoms which would mean most of the evidence against him would not survive admission in a Canadian court subsequently forcing the case to be dropped. A second argument against getting him back would probably come from the Prime Ministers Office. It is the opinion of the PMO that the most recent Federal Court decision encroaches on the power of the Prime Minister and interferes with Canadian foreign policy positions. The Federal Court has already, in several other cases regarding the Foreign Affairs Department, forced you to rescue Canadians from countries abroad. At lease two of them during the summer. Although the Canadian government did not like the courts ruling, it grudgingly complied with it. Technically, interference has already occurred as it was the position of Foreign Affairs not to get involved in rescuing two Canadians, one in Kenya and one in Sudan. In the end, they were forced to do so. In the case of the Sudan rescue, it was a Federal Court decision that interfered. In the Kenya rescue, the threat of a Federal Court of Canada case prompted the government into buying the citizen a ticket home, especially after a DNA test confirmed the persons identity. Therefore, the courts have already interfered with government policy. In the case of Omar Khadr, court proceedings include the following names: Prime Ministers Office, the Attorney General of Canada as well as other connected departments. With the PMO specifically named, one could infer that it is rather obvious that any court ruling with the PMO listed as a party, might interfere with what the PMO wants to do. Thus, it is a little strange from the PMO to claim direct interference by a court of law as an argument in a legal case. I hope the Supreme Court of Canada does not accept the case. If it does, results could go 50/50 for Khadr.
Full disclosure: I am a blogger not a lawyer although I happen to study law as a hobby. Any legal opinions expressed are a personal analysis of a legal situation.