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Running away out of the blue without any warning isn't standing up and correcting someone.
It was clear that Durandal gave Athrun the Faith autonomy so that Athrun wouldn't feel compelled to toe any line. Even at the most sinister of motivations of tricking Athrun into joining, it gave Athrun every right and reason to voice his views to Durandal openly. The fact that they had to ret-con insinuations of sinister manipulation into the story doesn't change that that was why Athrun joined it.
But Athrun didn't do that. He went behind Durandal's back when meeting with Kira and Lacus in secret, he never really talked to Durandal, and didn't do anything about correcting Durandal. He mostly kept it bottled up and let Durandal go ahead, and then fled after Durandal gave him an even greater opportunity. He never stood up to speak out and correct Durandal outright, and providing free and open contradiction was the entire point of him joining.
Stealing a mobile suit and fleeing in secret in the middle of the night was not what meant or intended by either side of that agreement.
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