I can't picture them as a ship pairing, however I can see Discord and Fluttershy being very close friends after the episode those two had. If he does show up in more episodes I can see Fluttershy playing the "Voice of reason" for Discord. Also known as the angel on his shoulder.
Yeah, they have a pretty dynamic friendship going on here. If Discord shows up in more episodes this season I think Fluttershy would be Discord's "Shoulder angel" considering that he is still Discord even if he is willing to be nicer. He would still be the mischievous prankster... Actually seeing Discord episodes with him trying to be helpful or solve a slice of life problem would be really interesting with a character like him.