2nd, its not the schools problem. It's the students problem. The school doesn't have to bend to the will of a couple of butt hurt students who went to the school for 4 years and never uttered a complaint about God up until they got their diplomas.
If a diploma offends you, then I have to say that your either A) a total loser with nothing better to do or B) someone who likes to start trouble where there is none.
It is a Christian school. Did the non-Christians who go there think that maybe at a Christian school, there might be references to Jesus or God while attending?
I mean is this such a far fetched notion to possibly conceive? Serously?