Reducing Intolerance, or Advancing It?

It seems that more and more frequently I skim the news, only to find another story about religious freedom slowly being eroded. This proved true again today.  It seems that Vanderbilt University, through its goal of decreasing intolerance on campus, altered its policies for registered student organizations.  The clause in question reads, "In affirming its commitment to this principle [of non-discrimination], the University does not limit freedom of religious association and does not require adherence to this principle by government agencies or external organizations that associate with but are not controlled by the University."  However, after a discrimination complaint in 2010 that was filed against a Christian fraternity, Vanderbilt began an investigation of every religious registered student organization on campus and deleted this clause from the student organization handbook.  The goal, no doubt, was to avoid any future "discrimination" by these religious organizations, but the result is something else entirely.
Although Vanderbilt has publicly stated that they "do not seek to limit anyone's freedom to practice his or her religion," this is exactly what will occur.  You see, through forced compliance to the student organization handbook, "membership in registered student organizations is open to everyone."  Furthermore, "everyone, if desired, has the opportunity to seek leadership positions" in the registered student organization.  This leads to a very serious problem.  How can an organization founded on a unique set of core beliefs maintain any sense of identity if it cannot require its members, or even its leaders, to hold those same beliefs?  Quite simply, it is not possible.
As a member of the Catholic Newman Center, a registered student organization on my own campus, this Vanderbilt fiasco serves as a dire warning. Through the noble aim of "reducing intolerance" on campus, Vanderbilt has completely obliterated the sole purpose of the registered student organization.  After all, isn't the point to form a group of people who share a common belief so that they may share their similarities?  Has it honestly come to the point that when similar people come together with a common interest. they can be accused of discrimination?