To be fair, any German clergy who objected had already been shot, gassed or sent to concentration camps. And on the allied side, the clergy felt that for once they had an enemy who was the embodiment of absolute evil. WW2 is an atypical war. A better example is WW1, where all sides were equally bad both from a political and a religious standpoint, with the possible exception of the Serbs, who were worse than average, and the Austrians, who were slightly better.
The truth lies between Bob Dylan giving politicians a free pass in the Universal Soldier, and those who assign all blame to the authorities; and it varies at different times and in different places. In 1930s Germany, which really had been taken over by The Mob in its most extreme form, very few individuals with liberty of action had access to the truth; and by the end of the War German soldiers knew if they deserted they and their families would be killed whereas if the Russians captured them only they would be killed, so they fought fanatically to the end. Many Russians knew Stalin was evil, but hoped that once the war was won he would be deposed. However, the tail of the Russian army consisted of very low types and left a trail of destruction and rape that their officers could not prevent, fuelled by NKVD propaganda, and there were plenty of Germans who were enthusiastic Nazis. There’s not much difference between them and US pilots deliberately shooting up civilians; every army has more than its fair share of psychopaths, and so I suspect does every government.