Sounds to me from the story that the problem is that they're blocking traffic in a high-traffic area. If that's all this is, they should be more reasonable. The 'commons' area from another report was the school cafeteria. Bottom line is that the school had no right to prohibit this activity or denying the requested organization and meeting of a prayer club during non-school times. This has been well established through court proceedings over the past several years.
The group was given brochures about the rights and responsibilities regarding prayer in school, [Principal]Sosky said, and was told numerous times it could meet for prayer but had to form a club with a staff adviser to do so. The participants also were assigned to meet in a room to not offend other students or interfere with their getting to class, and a teacher volunteered to be adviser, but the group continued to ignore the rules, she said. http://blog.oregonlive.com/breakingnews/2007/03/heritage_high_prayer_group_stu.html
Sounds like it was maximum of 12 students participating in the prayer group. Given that they were meeting before 7AM in the school cafeteria, it's hard to imagine how that could have been significantly blocking traffic. From what the prinicpal told reporters, it sounds as if the prayer aspect was the key issue, not the blocking traffic issue.