Is it possible to run the Mega on 3.3 Volts by supplying it to the 5V pin?
Not reliably. According to the datasheet, this is outside the "safe operating area".
At 16MHz, the safe operating area stops at 4.5V. Alternatively, the clock speed can be lowered to 8MHz for 2.7V (or maybe 12MHz for 3.3V).