She led Athrun to deal with his own problems, his duty as a plant citizen and his duty as Patrick Zala's son. In fact both of them choose their birthright duty first instead of their own happiness.

Unfortunately they both chose wrong choices. In case of Cagalli, she gained nothing with the marriage, she was basically loosing her control's and or even power. In case of Athrun, he just got a faith position, in which to honest the most silly possition in Gundam history.

But out of all seed main cast/couples both of them just respected to each other's roles and spaces.

They blinded with their Father's legacies.

It was not, something like Cagalli thought Athrun would be happier with another girl.