Peter Quinn was predictably outed as someone with a secret and untrustworthy. Estes pigeonholed him into this project as a contingency, and Estes "wants to kill terrorists" by any means necessary. He's essentially playing his Walden card with these hardline decisions.
Estes is the mole. Peter X (Quinn) is his right hand plus eyes and ears on the Nazir ops.
Saul basically called out Estes while the op was going down which leads me to think Estes will take measures to neutralize Saul, whether it be getting Saul fired (by blaming this last failed Nazir op on Saul) or by getting Peter X to take him out.
I think this last FBI/CIA Nazir op was legit and it is Estes and Peter X that are Nazir's guys on the inside. Hell Peter X may have never been a CIA analyst before Estes brought him in to oversee the Nazir terror plot investigation.
I think Estes is ultimately trying to extricate himself from being Nazir's inside guy. That is why he got Peter X to go kill Brody because Brody obviously knows that there is a mole and Estes can't have anyone who might figure out he is the mole. I think he still needs Brody alive until Nazir is taken in or killed though because Brody will remain an integral part of any such operation. Estes ultimately wants Nazir dead because Estes only cares about preserving his own ass.