To be quite honest the battles are apples to oranges.
Kira wasn't really fighting shinn, if he were then why was he running away?
No offense, but at that point you've gotta admit that the providence could have kicked shinn's ass let alone the freedom.
Also, we really don't know the time scale for athrun's battle, but considering the amount of times we see them hitting each other from luna's pov it may have been at least 10-20 minutes.
Kira and Athrun are both kickass fighters, and in reality are two sides of a really deadly force, a pacifistic side who prefers ranged combat to the aggressive close combat of the other.
Athrun is the more, "beat the shit out of that one really good person," as apposed to Kira's "beating the shit out of all those losers,"
Well, Kira was serious about fighting, it is the only way he could have been able to enter SEED.
Athrun's was 5 seconds, look at how fast Luna's expression changes.
Athrun also held off Legend Gundam ( a new more kickass version of the Providence, piloted by Ray Za Barru ), left because he had to destroy a superweapon. It all happened in Destiny. Athrun fought off Destiny and Legend together while in a Zaku, for quite a while until the Zaku just physically overwhelmed, not Athrun, but the Zaku, the Destiny's shield destroyed the Zaku's sword with Luna's sister literally physically in the way, she is in Athrun's cockpit. athrun also fought off three Gundams in a Zaku, also with the Zaku being physically overpowerd, but with Cagalli in the way. Athrun disabled the Minerva completely in 5 seconds, while Archangel and the Freedom almost got their asses kicked by them ( they went underwater to escape ), well Kira DID get his ass kicked in that battle, lost Freedom.
Yeah, once you see it my way....
P.S. Athrun does a lot of close combat., because of Justice's style.