Estinein is under the employ of the Dark Knight Aymeric
So Estinien right? He's generally considered to be missing and not dead, but a fugitive for having stolen The Eye. Yet he shows up at the side of the Lord Commander of the Holy Knights like he's still cool with the Holy See.
This could be seen as a hole in the plot, or perhaps an allusion to the unusual circumstances of Aymeric's position. He said himself that he is not a normal candidate for the Lord Commander stating that he earned the position because he "Swiftly learned to tell the difference between words, deeds, and beliefs."
Now lets take a look at the lore behind the Dark Knights as can be read here:

http://na.finalfantasyxiv.com/heavensward/
Essentially: Anti-heroes who serve justice to the corrupt political powers.

It is my theory that Aymeric is a Dark Knight. Or at least has a connection to them