The bootloader does USB. I don't think you can do USB on the 32u4 on only 8mHz.
You can however set the system clock prescaler to divide the main clock by 2, making it run at 8mHz. The bootloader will however still run at 16mHz, but that's probably still fine (though out of spec).
The AVR USB has a system clock prescaler, and the system clock can be divided by setting the “CLKPR – Clock Prescaler Register” on page 38. This feature can be used to decrease the sys- tem clock frequency and the power consumption when the requirement for processing power is low. This can be used with all clock source options, and it will affect the clock frequency of the CPU and all synchronous peripherals. clkI/O, clkADC, clkCPU, and clkFLASH are divided by a factor as shown in Table 6-10.
To divide the system clock by 2, set the CLKPS0 bit in the CLKPR register. The code for this would be something like this:
CLKPR = _BV(CLKPCE);
CLKPR = _BV(CLKPS0);
just note that everything runs twice as slow. So
delay(1000) will take 2 seconds. You'll have to update F_CPU somehow to fix this if this causes a problem.