I have recently found a declassified WW2 document located in the British National Archives that provides information about Canaris and how he ran the Abwehr. The document is a British intelligence translation of an Abwehr paper found in Belgium. The document relates to an Abwehr officers conference in Belgium on December 10th 1941. It was translated by Britsh intelligence (probably MI6) on 18th December 1941. The paper was clearly the text of a "pep talk" given by the Admiral Canaris to his officers in Belgium. The most interesting part is Paragraph 5. "Abwehr has nothing to do with persecution of Jews. The Ast's duties are to be carried out in a humane and soldierly manner. Activity against Jews is no concern of ours. We have nothing to do with it, hold ourselves aloof from it, do not criticise".
The rest of the document covers the general standards of operation and personal behaviour his officers should follow. The N.A. file number is HW 19/347.
I have placed a pdf of the paper here - http://cdmnet.org/technology/RSS/Abwehr-doc-1941.pdf