After all that has been written here we are still faced with the original question: how could Rav Shmuel have made such comments? We are talking about someone who is not only likely the gadol hador (in America) , but someone who many would consider the best person for a good aitza on any subject ( my son called him this week)and has a profound concern for klal yisroel. How then could he make comments which seem almost silly to most?
I believe the only possible answer lies in “sod Hashem l’yiraiov”. By this I don’t mean people shouldn’t get vaccinations. To the contrary I believe 99% of people won’t take Rav Shmuel’s advice and he knows that. But , somehow, I firmly believe,his comments will work out for the best for Klal Yisroel.
And, for the record, I’m a calte litvak.