Valkyrie is about the plot to kill hitler. It failed and the leader of it was executed. The person who was executed is like a martyr/saint of German culture lore. (anybody that was executed for being against the Nazis is now). And Cruise is playing that character.
He was banned at first because Germany considers Scientology a cult. And under german religion laws. (everybody gets federal money jews, catholics, lutherans, muslims etc.), anyway he's deemed the official person of the 'religion'. And since its labeled a cult, leaders of cults aren't allowed in the country.
Something like that.
Anyway they decided he wasn't the official spokesperson for the cult. They made some deal.