As to the denying thing, one change that might help is giving fruits trees 1-1 damage. Other food sources would share this as well, until they gain any upgrades they might have, like goblin factories.
This would make full deny more time consuming and harder to do, as the further you are away from 1 hp on the food sources the longer it would take to deny. It may also be harder to do successfully due to food sources not having the same amount of health as each other. The easier way of doing so, using your hunter, would put your hunter at risk of feeding as well.
This obviously isn't a permanent solution for ID balance, but it's a change that just might work as a band-aid for the time being.
This would change absolutely nothing as far as denial of feed goes(sure it would mess idiots up for a few days until they figured out how to make their denies work again). All you would need to do is attack twice with builder and repair and attack again then tell them to attack eachother a few times(or just leave them at 3 or 4 hp and que them so they all deny). Even if you came up with a system to make fruit denial not practical aka auto repair over time, people would just leave 1 shelter, big woop. This would just make fruit trapping/early fact/powerplant basing useless, aka make the game worse overall while adding no benefits.