If you're talking about Le Cellier, you can only sub a side that is listed as an accompaniment to another entree. You can't ask to sub something from the separate sides menu, like asparagus, without being charged for it. If you find steamed veggies on the menu accompanying another entree you can get it with your filet. There was a poster awhile back who asked to sub the asparagus for the rice, and it was not permitted.
Disney Special Diets will assist you with medical conditions or "lifestyle choices" like veganism. I don't think they are meant to accommodate just a preference to eat healthier. But you can contact them and ask.