Interesting suggestion, and it definitely pays to expand the word-search a bit, considering we can't hear Betty's "Marie" with our own ears.
As for Maru (or Mary), my guess would be that since Betty recorded the ward as "Marie," she heard the accent as being on the second syllable, i.e. potentially ruling out Maru or Mary.
"Marie" alternated at one point several times with "N.Y. [ostensibly New York]," so one possibility is that "Marie" is a call sign either of a contact or a station. Given where she was when transmitting, I'm not sure the first assumption would be that "Marie" would be a contact actually in New York (tho it's not impossible); I'd be more inclined to look into it being a contact aboard the USS New York, for example, captained at that time by either Leo F. Welch or Guy E. Davis.
Given the pattern (as best we can tell), calling "New York" first, and then adding "Marie," sounds to me as if possibly "New York" is the person Amelia is attempting to contact, and "Marie" is either a call sign for AE (or Noonan); however it's also possible that "Marie" was an agreed-upon distress signal. There was plenty of reason to not transmit information about a mishap in plain English; George Putnam himself liked to control things, and either for publicity reasons or for Earhart's safety over foreign seas might have preferred to use a private code word to indicate distress.
It is interesting though that only Noonan seems to say "Marie." Granted, the sample size is small, but for whatever reason only AE says "N.Y." and only Noonan says "Marie." We also get the sense that it may be AE at the radio helm, with Noonan's vocalizations being in the background, i.e. AE is possibly making more deliberate, official transmissions while Fred is being distraught. The takeaway would be that possibly "Marie" isn't an attempt to transmit a word, but rather something Fred is hollering in the background, whereas Amelia's repeated "New York, New York, New York" sounds purposeful.
Somewhere there's a note in the TIGHAR forums about Amelia's nickname possibly being pronounced "mee-lee;" there is one exchange in Betty's notebook where Fred says "Amelia...Howland take it away...Marie" which makes me wonder whether whatever he called Amelia simply sounded like "Marie."
But in my mind, at least, the "New York" stands out as fairly deliberate transmission, whereas the "Marie" is not so certain.
Just my thoughts today - been awhile since I was here, so I'm dusting off some brain cells. Apologies for any redundancies/errors.