So I don't have to do it all in crafttweaker (want to only cook it in ovens)

This will remove most stuff that is food from the furnace. You'll probably have to also add recipes to the oven for each thing removed because it won't be available to the oven as a furnace recipe anymore, but you can do that inside the loop for each recipe removed.

for recipe in furnace.all {
  if (recipe.output.isFood) {
    furnace.remove(recipe.output);
    // possibly add oven recipe here using recipe.input and recipe.output
  }
}

Does this meet your requirements?

What about a config option to do the contrary and prevent the oven from cooking food stuff?