Secondly, it is impractical to ask a bunch of students, many of whom probably don't have cars, to travel away from the school to another facility for an after-school event. By holding the event on campus many people who by their own free will wanted to attend were likely able to do so, when they would not have been were it held somewhere else.
And finally, you're simply diverting the issue to keep from addressing the central point: if a school opens its facilities for after-school use by student-organized meetings, it cannot discriminate based on the content of those meetings. So if they let an atheist organization meet, or a Republican organization meet, the must also permit a Christian group to meet as well.
If the church isn't within convenient walking distance of the school, I'm certain the school has a bus that transports sudents to the neighborhood where the church is located. And arrengements can be made among the parents to pick 'em up afterwards. If that is too "inconvenient", than I doubt that the parents have much interest in their child's religious training anyway.