I think Werner's death will hit Mike hard and lead him to realize that he can't get too buddy-buddy with his employees, especially if he has to shoot them later for whatever reason (like he tries to do with Walt in BB).

I don't think the Germans would blindly believe that Ziegler was allowed to escape or go home or whatever, because then what stops any of them from doing the same?

It seems like a half-measures kind of situation to me. They'll probably lock down the R&R and basically tell them to shut up and finish the job (because we know the job does get finished eventually), keep them on permanent lockdown, and then kill them all when they're done.