Nope. She did not agree to anything. Leliana had to deliver the message, which Celene would had to wait three weeks to a month for a response, while she thought it over.
"You asked for her support calming the templars and the mages."
"Indeed." Celene nodded. "And will she give that support?"
Leliana let out a breath. "She will," she said, nodding slowly, "but in return, she needs to know that this matter with the elves is under control."
That was chapter chapter 5. Leliana is one of Justinia's most trusted servants. She presents herself to Celene in chapter 1 with the words "I am her voice in this regard". So, unless you are saying that Leliana is lying in Justinia's name through all the book, that was an agreement.
I don't think she is going to be the big bad of DA:I since it has been implied that she dies at the meeting between mages and the Chantry.
The idea is that she might fake her death in that event. Then, decisions that were initially thought as 'good intention, bad execution' would be revealed as 'bad intention, flawless execution'.
"So there are problems in Kirkwall? No, no, don't send the Seekers, we need more chaos."
"So the Empress is worried about the mage-templar issue? Oh, my, of course I will speak in favour of peace during that ball in my honour. It's a shame there will be an "unexpected" incident that will derail it."
"And talking about the Empress, she's dangerous. Let's push her in the right direction, that is, to fall into Gaspard's trap, a trap so evident that even an elven servant can see it. Civil war in Orlais is also welcome."
"However, the assassination attempt may lead to me sooner or later. So let's put Lambert in charge of the investigations. There are already so many problems in the White Spire that the grumpy ex Tevinter Templar will start a war before doing his job."
"And now that wars are starting everywhere, I just need a lot of people in a place high in lyrium to open the biggest veil tear the world has ever seen. And who is better than the Divine to choose the place for a peace summit between some of the most influential and powerful people in southern Thedas? The Temple of the Sacred Ashes sounds promising..."
"Well, faking my death was a master stroke. The moderates in the mages and templars are all dead, and now the Chantry is headless. Chaos everywhere! Now I can do what I must without caring about... about... What the HELL is that story about a survivor?!"
It's a very far-fetched guess, especially since it's been hinted that the Inquisition was Justinia's Plan B.