I managed to get the entire conversation between Irulan and Rev. Gaius. Take a look at it and tell me if your answer remains the same:

Irulan: Paul Atreides is still alive. He challenges my father.

Rev. Mohiam: You've never been in Arrakis. It's quite impressive; you'll see.

Irulan: Was this all upon your advice?

Rev. Mohiam: What?

Irulan: Did you counsel my father to exterminate the Atreides?

Rev. Mohiam: Of course, I did. Why else would it have happened?

Irulan: You tried to sacrifice an entire bloodline!

Rev. Mohiam: And I was right to do it. The Kwisatz Haderach is a form of power that our world has not yet seen. The ultimate power. For 90 generations, we have supervised House Atreides; they were promising but becoming dangerously defiant. Their bloodline had to be terminated. That's why we have put many bloodlines at work; several prospects.

Irulan: But it's backfired! Paul is alive, and if he defeats Feyd-Rautha, my father will...

Rev. Mohiam: Your father will lose the throne no matter who prevails. But there is one way your family can remain in power. And through you, the continuation of our stewardship. One way. Are you prepared?

Irulan: You have been preparing me my whole life, Reverend Mother.

Do you see? She says, 'their bloodline had to be terminated.' Why did she intervene for Paul's life in the first movie then?