The Grail is a powerful organization full of powerful men. Allfather D'Aronique is the guiding hand of The Grail. Starr is the killing sword. And Eisenstein is its crafty, twisted brain.
Utterly committed to the cause of The Grail, Eisenstein was the man who initiated Starr into the organization. He was surprised by the young man's thoroughness and commitment to The Grail's principles, and recognized a potential greatness in him. With Eisenstein's help, Starr rose to the position of Sacred Executioner.
And by Eisenstein's hand, Starr very nearly fell from grace as Allfather.
After Starr's repeated disasters - the attack on the estate of Jesus DeSade, the destruction of their headquarters at Masada, the nuclear holocaust at Monument Valley - the ruling council of The Grail sent Eisenstein to investigate Starr's activities. If he discovered any fraud or wrongdoing, the Grail would strip him of his position as Allfather and likely have him killed.
Eisenstein brought two bodyguards with him. One was his giant fearsome dog, Jezebel. The other was a nameless Russian, a former member of Spetsnaz and very nearly as vicious as the dog. Together, they foiled multiple attempts by Starr to have Eisenstein killed.
With very little to go on, Eisenstein deduced the true scope of Starr's plan: he was responsible for the death of The Messiah, as well as the death of the Allfather, and planned to use the Grail's resources to set up Jesse Custer as a new Messiah. He had severed the bloodline of Jesus Christ, something that not even Herod was able to accomplish. This was a monstrous act, in Eisenstein's eyes, and he was ready to report back to the Grail Council on all of it.
So Starr killed him. He kicked the little man off a rooftop. He also managed to kill both the Spetsnaz guard and Jezebel, but not before the latter bit off his genitals.