For reference, this is the email I received from the admissions office when I asked about what I should do:
“MIT offers application fee waivers for international students. If the application fee presents a hardship for you and your family, request your Guidance Counselor/Headmaster/School Official to write a short letter to MIT simply stating that this.
The completed form or letter may be emailed back to this address in pdf format.
Proceed with your application as though the fee waiver has been approved. All fee waivers will be reviewed in January and the status will be updated on your MyMIT account tracking system.”