The calls for suppression of speech that offends religion (see here and here) don't seem to be limited to purely academic arguments. Here's an e-mail from the San Francisco State University to the College Republicans:

I am writing to you as President of the College Republicans to follow-up with you regarding the letter of complaint that was received by the Office of Student Programs and Leadership Development on Thursday, October 26, 2006, notifying the office of alleged violations of University policy. The complaint is in regards to alleged actions at a College Republican sponsored event, "Anti Terrorism Rally," that occurred in Malcolm X Plaza from 12-2 PM on October 17, 2006. The complaint describes alleged actions of walking on a banner with the word "Allah" written in Arabic script. I am writing to inform you that the Office of Student Programs and Leadership Development has concluded its investigation into the events that occurred on October, 17, 2006 in Malcolm X Plaza. The investigation was put in place to review the following alleged violations of University Policy as were addressed in the written complaint:
1. Allegations of attempts to incite violence and create a hostile environment
2. Allegations of actions of incivility (Standards for Student Conduct Title V, 41301)

Resources presented by interviewees during interview process for review include: 1. Standards for Student Conduct Title V, 41301
2. CUSP II Strategic Plan
3. California penal code

The Investigative report has been forwarded to the Student Organization Hearing Panel for review. The chair of SOHP ... is your contact person should you have specific questions regarding this review.... (I have cc her on this message). She will also be in contact with you regarding any questions and specifics regarding the review. You may continue to contact me regarding any general questions regarding the SOHP process. You can find the process online at http://www.sfsu.edu/~ospld/conduct/hearing_panel.htm. For a copy of the Code of Conduct, please see http://www.sfsu.edu/~ospld/conduct/policies.htm. I have also attached a word copy of these documents, to this email for your convenience. To review CUSP II, please see http://academic.sfsu.edu/apee/planning/plan05-10.php.

Please keep in mind Carl that you as a student organization have the right to have a representative at any stage of possible disciplinary proceedings. However, attorneys are not permitted as representatives in this process.

Sincerely,
... Director
Office of Student Programs and Leadership Development
Student Services Building, Suite 105
San Francisco State University

FIRE (The Foundation for Individual Rights in Education) has more:

The College Republicans "offense" took place on October 17, 2006, when they held an anti-terrorism protest in SFSU's Malcolm X Plaza. During the protest, several members of the group stepped on butcher paper they had painted to resemble the flags of Hamas and Hezbollah. Unbeknownst to the protestors, the flags they had copied contain the word "Allah" written in Arabic script.

As FIRE points out, burning the American flag, and stepping on it, "is without question a constitutionally protected act of political protest"; stepping on flags of Hamas and Hezbollah, even when they contain religious symbols on them — or for that matter deliberately stepping on religious symbols — is equally protected.

Note also that the university is not simply trying to prevent violence here (which it in any event should do by preventing and punishing the violent responses to offensive student speech, not by punishing the speech itself, at least unless it fits within the narrow category of individually addressed insulting "fighting words," which doesn't apply here). The university is expressly investigating (with the threat of formal sanctions behind the investigation) the possibility that the students' speech is ideologically offensive — creates a "hostile environment" and is "incivil[]." A clear First Amendment violation, it seems to me.

UPDATE: Here's a story about the rally in the campus newspaper.