Joseph, your translation does not match what you read out of it. To quote,
“[YU and Beis Midrash L’torah] are places of danger in terms of spirituality because they conduct themselves in a spirit of freedom. And what benefit is there to flee from a physical danger to a spiritual danger.”
Note that he said there is danger in both, but he does not say (or imply) that if one has a specific choice: Be killed or go to one of these places, that they should choose being killed. Rather, he says that the danger is similar in both places, and there is no use to flee because danger is at those places too, but he doesn’t say that the choice between certain death and YU, as it were, is death.