I mean...its his kid. She wasn't at the wrong place at the wrong time, she caused it to happen. She didn't mean to, but if she hadn't been there, Dajh would have been fine.
At the end of the cutscene he changes his mind obviously...but...think of it this way:
He's been essentially protecting this girl. He's been opening up to her, talking to her about his son, really taking her under his wing.
Then he finds out that she is the reason his whole life has gone to shit.
It's easy to recognize that it isn't really Vanille's fault when you're on the outside looking in...but what if it was you? What if your son just got turned to Crystal in front of your eyes, you never get to see him again. You're on the run from the government, and you've been protecting the person who's responsible for all of it.
He had every right to be mad.
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