Yes, Extraordinary Rendition is justified in fighting the war on terror, because it brings criminals to justice. Extraordinary Rendition does not allow other countries to play games or put conditions on the transfer of criminals. Extraordinary Rendition allows nations to hold people accountable for those who have committed acts of war against their nations.
Extraordinary rendition is a practice that facilitates distrust between nations and between nations and their citizens. In extraditing prospective terrorists and torturing them for information, nations only depict themselves as barbaric as the suspects they believe the suspects they have in custody to be. In publicly embarking upon the judicial process rather than privately, there are no holes for citizens or other leaders to questions legal motives or due process and alleviates the suspicious of ulterior motives.