As of 1.7.10c, HarvestCraft will have built-in right click harvesting. From a post on MCF:

You will be able to do the right-click harvest once 1.7.10c comes out for everyone, which is this Sunday

Need to figure out how to handle this on HO's side.

From the few tests I've done so far, it seems that setting B:rightclickharvestCrop=false in Harvestcraft's 1.7.10c configs allows HungerOverhaul to work perfectly as intended. No silly eating your held item while harvesting crops via right click.
I've left B:rightclickharvestFruit=true (default) for now but if I have any trouble with that, I'll change it.
I also left B:gardensdropSeeds=false (default) as well and breaking them still yields the 3 food items as before.

This is only going by my experience but with that one change to the harvestcraft configs, it's a non problem.

Doesn't seem to be an issue even with rightclickharvestCrop=true set in the HarvestCraft config.