Donitz was apparently opposed to the notion of a 'political officer' on board the U-Boats as far as I know, and Hitler famously once pointed out: "I have a reactionary army, a National Socialist air force, and a Christian navy.'
Although like most famous quotes, that one is open to a bit of interpretation. but if meant as a complaint, it is particularly ironic, since the middle-of-the-road Christian political parties were to a large extent instrumental in bringing the Nazi party to power, when voters of that ilk broke the political deadlock of no clear majority and put the Nazis in.
Nevertheless, there are many famous instances of Kriegsmarine (particularly U-Boat) men and officers displaying some highly 'un-Nazi' behaviour. Reinhard Suhren (commander of U-564), once famously shouted up to the quayside as his U-Boat came in from patrol: 'Are the Nazis still in charge?'
When someone shouted 'yes' from the quayside, he promptly put his U-Boat engines into reverse and backed away from the dock as a joke. And U-802 commander, Helmut Schmoeckel was in fact half-Jewish, but was allowed to serve nonetheless, so he's hardly likely to have approved of many of the SA's methods.
Having said that, other famous U-Boatmen were very much in favour of such methods. Joachim Schepke - noted for winning the Knight's Cross after sinking over 50,000 tons of shipping in just two days whilst commanding U-100 - is on record as having uttered many anti-semitic statements, although he stopped short of actually being a member of the Nazi party.
Oskar Heinz Kusch on the other hand, was reported by his IWO for sedition and defeatism (although his first officer - Dr Abel - may have been motivated by the fact that his first cruise on board U-154 with Kusch resulted in a poor report from Kusch and a denied recommendation for command, although a second report later proved favourable). Kusch was accused of taking down the picture of the Fuhrer from his U-Boat, apparently accompanied by the statement 'We are not in the business of practicing idolatry here.' Although some others on his boat claimed that he merely did such things to provoke discussion amongst his officers to relieve the boredom of a long patrol.
This incident provides some of the directorial inspiration for a similar scene with the IWO in the movie Das Boot by the way.
Nevertheless, Kusch was put on trial for sedition. His defence was not helped by the fact that he left the Hitler Youth early, although the prosecution failed to point out that he did in fact do so to join the Kriegsmarine.
Kusch was sentenced to one year in prison (ostensibly for the charge of listening to Allied radio broadcasts - something nearly all U-Boat crews did), but he refused to admit that he was guilty of anything and because of this, was subsequently sentenced to death and shot by firing squad in May 1944, the judge in that decision also being tried after the war in the 1950s, but eventually found not guilty based on the 'laws at that time not having been broken'.
However, as a postscript to this tale, many were not happy with that decision and in 1996 Kusch's record was wiped clean and two years after that in 1998, the City of Kiel honoured Kusch by naming a street after him (Oskar Kusch Stasse, near the Kiel Canal).
A plaque on Kusch's nearby memorial reads: 'His name stands for the many victims of the National Socialist system of injustice who died here and in other places. Their death is our legacy'.
Back directly to the topic at hand however, if you want to find out more about Donitz's motivations and the men of the U-Boats, I can recommend the books: 'Donitz and the U-Boats' (ISBN 1-86019-927-5) by (ironically) 'Bernard' Edwards, and 'Grey Wolf' (ISBN1-84176-312-8) by Gordon Williamson.
Anyway, welcome to the madhouse.
Chock