No I don't think that it is. Although there is no documentation as to whether or not it "borrowed" any idea from that episode if you come to think about it then you will see that the storyline of Bedtime Stories is pretty common.
There are a lot of times similar plots in movies, series and literature about little girls creating their own fantasy worlds and living in them. It isn't a new and uncommon storyline so to start believing that "Once Upon a Time" inspired by that specific episode.
If you come to think about it it is easier to believe that Supernatural got inspired by stories like "Alice in Wonderland" and "Pan's Labyrinth" (without of course believing that it actually did as I have said it is a pretty common storyline) rather that believing that inspired "Once Upon A Time".
But as there is no information about it everything is just an educated guess.
(Although if it actually had happened then I think that there would be some information about it.)