Not sure that that is what anyone was suggesting - for a time critical application most of us would just set up the hardware timers to do their thing in the background. They are entirely hardware based and not effected by whatever the software is doing elsewhere on the micro controller - until you want to effect them that is.
Look up the hardware timers in the datasheet, its not the easiest reading, but there are various waveform generation modes built in to do exactly what you want without software or interrupts getting in the way.
Duane B