I see that the MC9S08MP16 is documented to have FlexTimer peripherals with Dead Time Insertion DTI for motor control to help avoid shoot-through on bridge drivers.
http://cache.freescale.com/files/microcontrollers/doc/data_sheet/MC9S08MP16DS.pdf
But I do not see that MC9S08PA16 has Dead Time Insertion in its Flex Timer Peripherals.
Personally, I tend to favor using hardware to avoid possibility of shoot-through versus having to rely on always having proper code execution to avoid catastrophic destruction. I have relied on FPGA/CPLD to do this also, but I suppose the dead timer feature is put into the MC9S08MP16 for a reason.
Sorry that I cannot be of better help!
Mike