It all depends on where the insulation is. If you run exterior insulation down the outside of the foundation wall to bottom of footing and condition the crawl space, this would be doable. But if there's no conditioning, the crawl is cut off from the interior by insulation, and the crawl is vented to outside and can freeze (even if vents close in the winter, the temperature can still drop), the interior footings need to go to frost depth, too.
Your drawings should reflect the requirements of the building code and your engineering judgement. You're not a draftsman for hire. The owner does not get to dictate the detailed content of your designs and drawings just because he/she doesn't like what they are required to do.
Option 1: leave drawings as is and tell him not to do it. This is probably the easiest. But I would say don't give him any of that "at your own risk" stuff. Tell him no.
Option 2: Drop the footings an additional 32" to maintain frost depth even with the crawl dug out.
Keep drainage in mind. Not sure how things are where you are, but around here this would be (and, as I've witnessed a few times, IS) a nightmare for maintenance. I like FEMA's guidance for this: crawl space should be a minimum of 1" ABOVE the lowest adjacent, exterior grade. Combined with a good vapor barrier and good grading, that keeps standing water from sitting in the crawl and rotting everything out.