It's usually discouraged because that's not the way most actual books appear. Also, in my opinion, it's a lot more touch and go, whereas a narritive style book usually touches base more on feelings, emotions, thoughts, environment, and considerations. Script is also used a lot more for humor purposes, and from seeing your fic, it's a lot more on the serious side.
Fan Fictions in Script can be quite good though, Hoenn Mirror World is a good example of a nicely written fan fiction in script format. Yes, it's your fic and you decide what you want to do with it, but I'm sure Oni is just trying to point out to new authors that Script format really shouldn't be used as a crutch to write a fic faster.