Its hard to be clear on details. From the little we know it sounds like Thordan and his Knights did it to take the power of a celestial dragon for themselves. As to the why, its assumed that it was out of greed. Weither that was all there was to it or not isn't clear at this point.

As for the other Elezen, there is no guarantee they ever had the truth revealed to them. Indeed the opposite seems to be the truth. Thordan and his knights could easily claim that the dragons attacked them. Alternatively Thordan could have been part of a group of Elezen who felt that either they were becoming effectively servants of the Dragons rather than partners or felt that the differences between dragon and elezen meant that eventually their shared civilisation was destined to fall apart anyway. We see on the dragon side of things at least Nidhogg never liked the humans to start with. He pretty much says 'I told you so' during the echo vision.

Im kind of hoping they will delve further into this during the patch cycle.