Exactly.  If the Courts had ultimately arrived at the same or greater remedy, but we, as Canadians, had the benefit of the legal rationale for it, any payout would be far more palatable.

Khadr was in prison because of his own decisions and actions.  And while his Charter rights were deemed to have been violated by a few visits from DFAIT & CSIS in 2003/2004, the burden of proof is on him to demonstrate that it had any material effect on his situation.  Much less his allegations of 'conspiracy'.

Arar, on the other hand, was put into prison and deported to Syria primarily due to the negligent actions of Canadian officials.

Arar was entitled to everything that he received and there is a world of difference between his situation and Khadr's.  

Little wonder that the federal government also treated the two situations differently.