Perhaps you should read the entire article and not just the lead paragraph synopsis.    

First of all, the SCC was ruling on the Federal Court and Federal Appeals courts order that the Federal Govt demand Khadr's repatriation.

Khadr was being held in a foreign jail.    Because Canadian courts cannot order a release from a foreign jail (this is up to the Federal Govt who retain perogative powers over foreign affairs including all the representations to foreign govts) the SCC concluded that it was outside the power of our courts to demand repatriation as a remedy.     Thus the SCC declared that Khadr's rights had been violated but left it up to the Federal Govt to provide a remedy for this breach.    This was in 2010.     The key part of this ruling is that Khadr's rights had been violated by our Federal Govt.      The second part you miss is that our current Govt finally provided a remedy for this breach.