It wouldn't be surprising for operational speed to be below maximum rated/theoretical speed.
But anyway, here's some info: According to the GundamOfficial timeline, Kira stole the Freedom on May 5 and joined the battle at Alaska on May 8. So it took about 3 days for the Freedom to go from the PLANTs, located at Lagrange point 5, and wherever Alaska was relative to L5 during that time period. Of course, I doubt Kira, even as a Coordinator, would spend all time at full speed.
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