As I said, I know perfectly well what he was trying to do. But in a case like this, where it is apt to be misunderstood, he should have made sure he was super-clear beforehand what is and what is not happening. And he should have made sure none of the speakers were active mishkav-zacharniks. This was a slow-motion train wreck that anyone could have predicted.
The writers of the Beacon claim support from a lot of YU students for their writings. You can’t just brush it off with “nobody listens to them anyway”. It is clear they thought they were representing a large part of the student body. And in fact, this same student body cheered on an active mishkav-zacharnik and gave him support. Finally, the atmosphere inevitably affects people. A school in which a large part of the student body thinks mishkav zachar and gross violations of halacha are ok is clearly not for a frum person. Saul Lieberman was Orthodox too, but nobody would have said to go to JTS.
Mistakes happen. Some of them, like YU, endure for years.