Jothar,
When very few visas were available even before the war broke out, R’ Chaim Ozer Z’L had to make the decisions as to who gets them. When similar situation occured in the USA during the war, the Rabbinical arm of the Vaad Hatzala were breaking their heads deliberating upon who shall live and who would die. One of its senior members almost refused to state his opinion, saying that “only R’ Chaim Ozer had the achrayos to pasken dinei nefoshos like we are attempting to do”. So, in the end, there are halachos in pidoyn shevuyim regarding who comes first. Therefore, talmidei chachamim of the greatest caliber were issued the few obtainable visas.
It wasn’t just that the orthodox saved only their own. There are actual and pertinent halachos on this matter, and they were followed. This seeming “unfairness” was not arbitrary, but decided by Chazal, and one of the p’sakim in the Gemara is “Aviv veRabo, Rabo kodem”.
One doesn’t have to like it; it’s a din, not any different that when a rov tells someone that their dinner is treif and needs to be thrown out.