That's funny, because my dd (11) didn't like the adult entrees at Sci Fi Diner and Plaza restaurant and was able to get an adult app, child entree, and adult dessert. We found the CM's were very accommodating to everything we asked about and we even were able to use our dessert for a milkshake to go at Liberty Tree, Sci Fi, and Whispering Canyon. It wasn't the best use of points value wise, but it made us happy and we enjoyed everything. Maybe the CM's you came across were a little more "by the book".
I don't think this is giving away any protected "secrets", so I'll share somthing that Tour Guide Mike says. He says that at super-busy times, WDW obviously really "staffs up", so you're more likely to encounter new or inexperienced cast members. I bet the restaurant employees they ran across who wouldn't let them buy childrens' entrees fit into that category.