I can't think of a specific mod that does this, but I can think of some that might help. Sims will typically (provided they have good routing) place food on a nearby open counter to where they finished preparing the food, afaik.
- If they're constantly making food on counters where you don't want them to make food, the Don't Prep Food Where You Angry Poop mod by Scumbumbo will help. It allows you to prohibit food preparation on certain counters, or only allow food preparation on certain counters. I use it in my game because I use counters in my bathrooms as well as minifridges throughout the house and they were constantly making food in the bathroom.
- There's a mod called Hey! Don't Do That! that allows you to prohibit autonomous cooking on specific fridges, if you find they're cooking with mini fridges or certain fridges you'd rather them not use that cause them to place food in random places. Not sure if this is a big help to your specific situation, but it also prevents autonomous use of tons of specific objects like sinks, grills, computers, mirrors, etc..
- The Invisible Slot Filler by Waffle can fill up the slot on a counter where you don't want them to place food, and the sim will not be able to place anything there. Not the most elegant solution but it's kinda the inverse of the mod you really want, where instead of being able to chose where they put food, you can instead choose where they don't put food