The intent was not still there. Isabela did not try to get you killed, or start a war, and we have no idea how many people she's killed or who they were. She's nothing like Petrice.
Isabela knowing made you the fall person for the entire situation when she KNEW that war was breaking out over the entire thing and even lied to you about not running off with the book which you needed to try and stop the entire thing from exploding. Not to mention that she knew about it even before meeting Hawke, hence why she doesn't want to go see the Qunari on the off chance that they would know who she was.
Furthermore, YES she did knowing start a war. She knew what the book was, she knew what the Qunari would do to get it back, and she knew that those that wanted the book wished to use it as propaganda against the Qun and to instigate all out war. Yet she still stole it, kept it and tried to run off with it when she got it back.
Not saying she's the same as Petrice. What i'm saying is that she LITERALLY did all of those type of base things that Petrice did. The difference is that she isn't an insane religious zealot and is instead a very selfish individual who only looks out for #1 unless you change her opinion by putting up with her constant betrayals.
Fact is that the Arishok became rather tame as soon as he got the book and if you hand over Isabela he leaves in peace. Had Isabela never stolen the book or it was returned earlier than the Arishok would have packed up his followers and left without a fight or fuss or never even been there in the first place.
The Arishok was also highly patient, he hated the city and there were fanatics killing his followers. Yet he did nothing for 4 years, it was only when he finally had enough, and the book still not being found at that point, that he snapped.
Furthermore...
Novels and Comics make it clear, Isabela killed a ton of innocent people over the years and did murder a ton of slaves when she tossed them overboard, while still chained, to their deaths.
That's not Isabela's fault. BioWare's been dropping hints for a Qunari invasion since Origins.
Doesn't matter, Isabela gave them an excuse and she knew very well how important that Book was and what those that wanted it stolen planned to do with it.
She didn't care, all she cared about was her own hide and making profit. Had her ship never been sunk than she would have delivered the book as planned and a War between the Chantry and the Qun would have started before the first year of Hawke's service with the Theives or Mercenaries was up.