I've always felt that the events in FFVIII are always how things happened. There was no changing time. Since Squall & Co. had fought and defeated her knowing she was from the future, everyone just kept an eye out for that big bad Ultimecia that would inevitably come into existence. And so she was persecuted before she had a chance to do anything wrong. So she was just like "what you want Ultimecia, well fine then you get Ultimecia " She was just an ordinary woman who became a sorceress during an era where they were more feared and hated than ever.

But that's just my opinion.