Thanks for the advice MorganS, unfortunately I neglected to mention that there needs to be a controllable delay between the pins going high, preferably from (as close to) 0 to ~170 uS. The reason being the initial pulse is a "zero-phase" marker from an AC current source, and the resultant pulse from the Due needs to begin at a programmable phase.
So my plan was:
phase marker pulse -> ISR sets "go" variable to true -> Timer interrupt with "go" now true, waits a programmable number of ticks, sets output pin high, waits another bunch of programmable ticks and sets pin low. -> await next phase marker pulse.
If getting the delay less than 1 uS is unrealistic then I can just make it wait for a complete cycle in addition to programmable delay