Ok I have to throw this out there because I love me some speculation and it doesn’t seem that far off when I start connecting the pieces.
This line keeps coming back over and over in my mind:
“What Ronan knew and never told still lingers in the Dream.”
What if the seeds that existed in the cave that Ronan found weren’t actually seeds, but dragon eggs? More specifically, eggs from Mordremoth? Because Ventari and Ronan raised the tree with care, kindness, and a moral code, it grew into a being that was opposite of it’s parent. This wouldn’t necessarily make her a Champion of the Dragon, but due to her connection to Tyria, to its life, and to Mordremoth, she is definitely in a position to know of her true origins.
There are other lines that seem to suggest the Pale Tree is aware of this fact about her Sylvari:
“If you are not one with what you were born to be, you are lost. Worse, you are dangerous.”
“Please: go no further. In seeking to comprehend the forces that shape us, you will unleash them. Society cannot withstand that.”
It’s possible, in the same vein that the Great Destroyer was Primordius’ champion, that the entire race of the Sylvari was supposed to be Mordremoth’s. Instead, it could be that the existence of the Pale Tree inhibited his growth/consumption/awakening due to its peaceful and non-invasive nature. Consider how it grew; it’s roots spread across all of Tyria. Who else’s roots have recently started doing that? Thanks to Malyck, now that we know that Sylvari can be created outside of the Pale Tree, this seems to be a more likely theory. It would stand that Mordremoth would be most driven to uproot and destroy this opposition (much like Kralkatorrik went after Glint and Zhaitan went after the other sentient races) which is why he attacked.
The Sylvari that are turning to nightmare are ones that are embracing Mordremoth’s nature already inside their being. They are seeking their “true” nature, allowing the corruption of the dragon, which is why they will always be severed from the Dream of the peaceful Sylvari. The anomaly in this equation is the Pale Tree and her Sylvari, who are not acting as they were created to, whereas the NC and the others are embracing what they are.
As for the vision provided by the Pale Tree, I think it was nothing more than a glimpse of what would happen to the world without her influence. It clearly shows in the beginning that she is fading, and starting to die. The remainder of the cinematic is the consequences if we let it happen. Five pillars of fire and energy, five prominent civilizations to stand in the way of the dragons.
TL;DR; Pale Tree seed was dragon egg of Mordremoth, and the race of Sylvari were supposed to be his herald/champion. Pale Tree is nice, so she must be destroyed by the true Sylvari, the ones embracing Mordremoth and the Nightmare.