The lever here is a simple one, not a membership constraint, but a leadership constraint.
For example, a foreign language club would likely insist that because its meetings are conducted in a foreign language, its leaders must speak that language. Thus it is not discriminatory for that to be a requirement.
Likewise, in a Christian club, they could create a competency requirement for the subject matter, for all leaders. That this competency would exclude students who were not scholars of Christianity is not prejudicial.
The competency would likely require Christian explanations of the miraculous to the point where it would gag any atheist or non-Christian.
that foils the mission of such a club, Personally I would have the Christian club members join every leftist club on campus and run for offices in the clubs.