Why? What are the specific definitions or margherita and marinara that don't allow these modifications? Without undisputed definitions, this is just irrational dogma. Black coffee by definition excludes milk, cheeseburgers by definition include cheese, but for margherita and marinara, this is not obvious at all.
A foreigner ordering margherita with garlic is violating our sense of taste and altering a template that doesn't allow such distorsions.
As a counter example, you can add without problems an egg on a margherita; it becomes a "Bismark pizza", but it's fine since the egg plays well with tomato and mozzarella. Any modification that is an enhancement, rather than a distorsion, is alway welcomed.
What is fine for one person, doesn't make it fine for everyone else. Personally, I would have been incredibly offended, and told them so. After-which, I would have cancelled my order, promptly left and gone to another pizza place that would give me what is asked of them.
Trust me, nobody would have complained for "a pizza with tomato, mozzarella and garlic". A "pizza margherita with garlic" is a very different thing.
TL;DR - Who cares?