Nigel, You're right about the interrupt latency. As for "fixed intervals" provided by the timer, that depends on the timer. Those I've used can resolve down to a single clock cycle - far better than any software routine.
Depending upon the timer and whether or not he needs a single pulse or a regular waveform, he might just be able to program the timer and let it rip (with no ISR required). But again, all this depends on the hardware he has available. The best advice? Read the databook.