There actually is a fair bit of doubt that he threw the grenade.  Here's something from an old Globe article: " A U.S. military commander altered a report on a firefight in Afghanistan to cast blame for the death of a Delta Force commando on a Canadian youth who was captured after the shooting stopped, a defence lawyer said Thursday.
The lawyer, Navy Lieutenant-Commander William Kuebler, made the allegation at a pretrial hearing as he argued for access to the officer, identified only as “Col. W,” as well as details about interrogations that he said might help clear his client of war-crimes charges."
The same Globe article goes on to detail that in the original battle report, the man who threw the grenade was killed. 
Khadr was unarmed and badly wounded when captured.  If had ever had a fair trial, we might know whether it was even possible for him to have thrown a grenade given the extent of his injuries.