I couldn't tell from the posted article whether the 12 suspended were the whole group, or just the ones who refused to stop/move after being asked to. From the other article that I posted a link to, it's pretty clear that there were only 12.
Remote location is an issue only if it distinctly different from the locations offered to favored groups. If most student groups are given rooms in a central area of the school, with which all students are familiar, and which has high foot traffic which would tend to publicize the existence of the groups, and the prayer group is offered a room in an area where most students rarely if ever go, that would be a problem (like on a hall with administrative offices that have no student contact, or in an overflow trailer classroom on the perimeter of the campus). A lot of high schools are VERY large these days, often with multiple buildings.