Debra Saunders, an S.F. Chronicle columnist, writes:

This story starts with an "anti-terrorism rally" held last October on campus by the College Republicans. To emphasize their point, students stomped on Hezbollah and Hamas flags. According to the college paper, the Golden Gate (X)Press, members of Students Against War and the International Socialist Organization showed up to call the Republicans "racists," while the president of the General Union of Palestinian Students accused the Repubs of spreading false information about Muslims.

In November, the Associated Students board passed a unanimous resolution, which the (X)Press reported, denounced the California Republicans for "hateful religious intolerance" and criticized those who "pre-meditated the stomping of the flags knowing it would offend some people and possibly incite violence."

Now you know that there are students who are opposed to desecrating flags on campus — that is, if the flags represent terrorist organizations....

As to the disciplinary action contemplated by SFSU, and FIRE's reaction to it:

The university's response [to FIRE]? Spokesperson Ellen Griffin told me, "The university stands behind this process."

And: "I don't believe the complaint is about the desecration of the flag. I believe that the complaint is the desecration of Allah." ...

Sounds to me like SFSU is acknowledging that under SFSU rules, desecrating Allah — or, to be precise, desecrating religious symbols — is indeed prohibited. Everything old (here, blasphemy bans) is new again.