I guess I can understand the idea that some kids might just order anything they want and Mom might balk at it. Some people really infantilize kids.
And legally, a 12yo can't be held to any contract they make, so if the kid orders something and Mom refuses to pay (thereby refusing to take over the contract), then the deli clerk has to put the food back. (which in the case of ordering 1/4 lb. of ham really shouldn't be a problem!).
But to ignore her for 5 minutes, yes, that's rude. If the clerk is uncomfortable entering into a legal transaction with a kid, then she says, "I'm sorry--is your parent here? Can I talk to her?"
So, ok, but when you've said, "She can order anything she wants," then you HAVE taken over the contract, and she was really rude not to go ahead and simply fill the order.
Getting the manager to endorse your point of view was perfectly fine.
I'll even give you a pass for sounding kind of testy.