Assuming magic can be replicated and analysed, which in almost any setting it can be, I see them eventually coming together. Just because magic doesn't follow our rules doesn't mean it follows no rules, and if it follows rules at all, you can do science to it.
Doesn't mean you can't have conflicts.
"The Eternal Flame of Arnor is sacred! You don't use it to . . .boil water like a common kettle!"
"But think of the potential! With the steam generated, we could power the entire cities power needs and heat the temple complex! All without any pollution whatsoever!"