It may well be the R”Y simply feel powerless to fight this fight, even though they believe it to be wrong. They may well fear that it may chase some away from the Yeshiva, and it isn’t worth that trade-off.
So, you’re saying that the R”Y would allow their bochrim to violate a mitzvah d’oraissah for fear that they won’t attend?! I know that I’m far too feeble-minded and far to corrupted by my modernity to cogently figure this out in a hashkafically pure way, but that just doesn’t sound right to me.
The Wolf