Jeez, I don't like either alternative.
Leaving the brake system dry doesn't seem right - the cast-iron surfaces of the MC and calipers might corrode, especially in your humid Boston climate.
Filling the system is probably the lesser of the two evils, though the brake fluid will absorb moisture over two years.
Best bet is probably to fill it, to work the brake pedal from time to time to move the components, and probably to replace the fluid when it's time to start driving.
Alternatives: finish it quicker or move to the desert.