It is unlikely that A) the German sailors were aware of mass exterminations of either Jews or anyone else. B) they had any real choice in supporting the war. The Nazi gov't was short on man power for the war effort and by 1944 when most of these boys were conscripted, the war was pretty clearly a lost cause. We were trying to kill them, no big surprise on that either. However, the politics of the dead is moot. That they fought bravely and died for there country is cause enough for respect. The U-boot service had a 75% casualty rate, the highest of any service in any military during WWII and they remained a cohesive force until the very end. Why this particular boat failed to observe the surrender will never be known, but they were part of a very disciplined and effective fighting force. They deserve a level of respect.
US Marines killed on Tarawa atoll in WWII battle finally repatriated thanks to Mark Noah of History Flight - CBS News
Take a look at how we expect our war dead to be treated. Germany lost over seven million people in the war, more than thirteen times the casualties of the US. At the end of the war They did not have the resources to repatriate every body. But, they did express a desire that the bodies be left alone.