I'd say it is the storm that is being "set to flight." The storm front is what's going north, and the rain is simply following that; thus, the storm is making the independent movement.
I'm guessing that the phrase "set to flight by bells" is metaphorical, as if the church bells signify a time when there is not supposed to be rain, and thus the bells cause the rain to leave. I could be completely misinterpreting it, however. In this sense, "set to flight" would mean driven away or caused to go away.
That was more or less my interpretation. On a previous sentence the author refers the noise of the bells as louder than the rain and the thunder.
So its very likely it would methaphorically "brush the rain away".
It could be the rain, or the storm front, or both, that are set to flight. It is impossible to say because in reality neither rain nor fronts are scared of bells - this is a specimen of pathetic fallacy. http://en.wikipedia.org/wiki/Pathetic_fallacy