I don't think you were rude for ordering when and where you did. It seems a bit excessive to come back right out of the gate with, "use BOTH sides to order, like every counter service," though.
I'd like to think I would have assumed it was her first visit and she didn't know that (because it's not something generally done outside of WDW), and said something more along the lines of, "At counter service restaurants in Disney World, it's set up so you form two lines and order from both sides." And then maybe asked the cashier for confirmation so she'd see it wasn't just some rule you made up.
Yes, maybe she was out of line to mutter to her husband, but I think the way you responded may have come off as, "You stupid idiot, what kind of moron do you have to be to not already know this thing that you've probably never experienced before?" I'm sure that wasn't your intention, but it might have come off that way.