I don;t think it can. If Mass Disruption affected High Waking, it would be a terrible experience trying to jump out of a system. Needing to travel to a 'Jump Out Point' where the effects of the systems' gravity doesn't interfere with your FSD would be burdensome.
Your only choice would be to artificially apply it between ships, or target Drives or FSD during the spool up time for the High Wake. I know which way I prefer.