I wouldn't have all six magical types regarded equally in a religion, personally. Only because religion is rarely as welcoming of new discoveries as science is. Maybe they've insisted for a long time that one of the elements didn't exist, say. You can make the wind blow harder? Psh, yeah, okay crazy man, that's pagan talk. It'd be easy enough to dismiss or persecute users of one element if such users were rare and the church (or whatever institution you have) decided they didn't like those people.
And the religion's stance on elements would probably have an effect on whether mages of a particular type are accepted. You could have your mages grudgingly accepted only because they're so useful. Sort of like a known ruthless assassin -- yes, he's got helpful skills, but most people would feel uneasy about being left alone with him. Maybe mages are stereotyped (ie. fire users are pyromaniacs, they'd burn the house down around you while you sleep just for kicks) and those users lend their services to battle because that's a socially accepted use for their skills? Maybe a way to gain back a bit of honour? Humans tend to mistrust and malign those who are different.