Roy,
The MMA8653FC signals an interrupt by driving the INTx output either low or high depending on the setting of the IPOL bit in the CTRL_REG3 register. A selected interrupt pin on your MCU needs to be configured in accordance with this setting (falling edge or rising edge). To deassert the interrupt on the MMA8653FC, it is necessary to read the appropriate status register for the embedded functions or X, Y, Z data output registers (0x01 - 0x06) for the DRDY and FIFO. I do not recommend to perform these I2C reads and any operations with the data in ISRs, I would leave it up to non-interrupt code. It is a good practice to keep ISRs as short as possible.
I hope it helps.
Regards,
Tomas