My logic at the time was as follows:
Maria is a relatively common name in South American countries, Brazil included. Mary (the character) is of brazilian descent. The name Maria, while not common, is also present in Japan due to phonetic similarities. Hence, her parents named her Maria.
Mary is the English form of Maria.
Normally, the pronunciation isn't the same ( meh-ree vs. muh-ree-uh) if you do it the english way. If you pronounce Mary the way a person who speaks portuguese or spanish (maybe also japanese) would, they'd sound a bit more similar.
Teeeechnically, the name should be written as "Mari" (muh-ree), but "Mary" is cooler.