People have different views about God and no one religion should feel superior over the other religions. Over the years, even before civilization, different communities held different creation stories and in most of the worlds populace at least believed in existence of supernatural being (GOD), though variation on whom he could be associated with.
Prayers and religion have by far been used to give hope to the desperate, maintain discipline and order in the society through observation of religion expectations as well as being an effective tool of bringing people together especially those who share the same religion. This is a positive attributes have been witnessed during religious gatherings by people coming together; helping one another and even observing the doctrines.
People have become more dynamic and it is common to find people/students from various religion of the world schooling under one roof. This dynamism, calls for critical balance between what and which religion should prevail. Any attempt by the authority concerned to indicate such supremacy can end up disintegrating different religious groups further rather than achieving the mission of unity and peace. It is very evident how some countries have fought on this matter like what has been happening in Sudan for many years.
It will be for that reason, paramount for principals to appreciate the fact that people have different beliefs and since it might be impractical to allow all religions represented in prayers, to my opinion to overcome such challenges, no religion should be superior to one more. It will thus be wise not to have such prayers from any religion. This might ignite sparks where parents /guardians might feel their children are not getting religion teaching. The best way to deal with such complains will be, by providing a balance sandwiched between all religions and this can be achieved through letting all students to pray silently between himself/herself for a specified time i.e a minute or so. This will not undermine any religion and at the end of it all, all will have been given opportunity to communicate with their creator.