There is zero cost whatsoever. The room was originally designed with certain school attendance volumes in mind. If numbers have declined due to local demographics, and taxpayers (including Muslims ones) are still funding the school board, it makes complete sense for the school to:

1..) allow the kids to use that empty space, since its not interfering with any other activities
2.) it helps the school fulfill legal obligations without any extra costs

The critical point of distinction here is that kids who are already in school are asking to use an empty room for 30 minutes. They are the appropriate stakeholders in this discussion. 

Homeless people or anyone else wanting to sleep in the school at night are not stakeholders in this discussion. You can keep bringing up that red herring as often as you like, it won't make a difference.