Chris Carter has made it no secret that he is a man of faith and that Scully's struggle with her own Catholicism is likely a very personal issue for Carter to write about. Scully's struggle with her own faith and with the Church's doctrine is a theme that Carter in particular clearly finds inspiration to return to on a regular basis, but "Miracle Man" is possibly the first episode to really deal with Scully's Catholic upbringing and struggle between her work as a scientist and her faith in God.
Not surprisingly, "Miracle Man" is rated quite low, not just at the moment, but it was never a widely-liked episode. I say 'not surprisingly' because religion isn't many people's favorite topic- atheists tend to dismiss anything with religious undertones as stupid and outdated, and very devout people tend to get upset at even things like "Miracle Man", something clearly written by a Christian which still brings into question some of the more unusual practices and phenomenon surrounding religion, or more specifically extreme cases of religious devotion.
All that said, "Miracle Man" is not just a smart script that opens Scully's character to many of the aspects which would later become key to episodes focused on her, it's also a fun little thriller script, and one with weighty and well-written enough subject matter that it doesn't become laughable as several season one episodes do. "Miracle Man" is quite good, really.
8/10