So some students are prejudiced against Christians and the school wants to support them in their bias? That's real open minded of them!
The undertone is here that R.A.s are expected to deal with students who are sexually active or considering sex, and may be charged with making condoms available. The college is probably worried that an R.A. who makes himself a Christian leader within the dorm would not be trusted by students who are testing their limits (and in some cases, the law) with sex and alcohol. The point of R.A.s is that they're the "cool" front line of defense for an administrator expected to keep these students from killing themselves by doing something stupid.
And to anticipate the response I'll get to that, loads of freshmen have sex and drink beer their freshman year without dying as a result, so I don't think that taking away an R.A. they're comfortable talking to would actually save lives.