Shaf, the "services" are not held over lunch time.  My understanding is that they are conducted after lunch, during a class period.
If you accommodate all religions where does it stop?  Muslims are required to pray 5 times a day.  Is that next: allow for those prayers that fall during school session every day?  I don't know how Hindus practice, maybe there is something they should be performing during the day? Every religion has a way of practicing which could take place during school session.  If concessions are made for all religions during school hours, there is constant disruption of the educational process.
I think there is a difference from cutting class to goof off and cutting prayer.  Some were probably doing it to take a "break" and return to class, others were leaving the school under the guise of attending prayer and cutting prayer and classes, and there were students attending prayer and returning to school.  
When you get caught cutting class in a public school to goof off action is taken by the school and usually parents are notified and the student is spoken to.  When a student attending Catholic reglious instruction doesn't attend class, parents are notified by the Catholic school that their child missed a class.   There is monitoring of attendance in both the public school and the religious school.  Whereas there was no monitoring for those students who were released to attend prayer at the mosque.  When cutting prayer, what action is taken?  How do  you "penalize" a student for cutting prayer?  Who addresses the problem?  The public school has no jurisdiction in that department and I'm sure the mosque doesn't take attendance and become responsible for those who leave public school to attend, or not, the prayer.  So, to solve the problem, you move the prayer from the MOSQUE to the class room to ensure that those students who choose to pray can.  I guess it came to light only when school teachers  or administration showed peaks in absenteeism on Friday afternoons. 
 
  Apparently many Muslim students don't pray and remain in class, if you go by the numbers.  If it's an option to pray, why do those girls who are menstruating go to the make shift prayer room, just to sit in the back and not pray???