I have no issue training pups/dogs with food. What I do have an issue with, is people/trainers training frantic dogs with food, or causing them to become frantic!
Don't just look at what you can get a dog to do using food, but understand the deeper emotional and psychological impact your training maybe having on the pup/dog. This awareness should be your number one concern when training your dog.
We need to be very aware of the power of classical conditioning, the conditioning of involuntary unhealthy psychological and physiological states in the pup/dog, whilst using positive reinforcement, whether it be with food, toys or even praise.
I never just look at what the dog is doing for me, I am firstly acutely aware of the dogs current emotional and psychological states. The dogs current state will dictate to me the type of reinforcement I will use to reward a dog for appropriate behaviour, if any.
If I am working with a dog that is frantic, overly anxious, and can't control its impulses, my preferred method to calm the dog during training, and to bring the dog back into a more focused and clear state of mind, and at the same time rewarding appropriate behaviour, is using negative reinforcement. Negative reinforcement is one of the most powerful processes to help bring a dog back into a more balanced state. Negative reinforcement, for those that don't understand, is the process of removing something to encourage an appropriate behaviour. For example we can use leash pressure to cause a level of discomfort at the dogs threshold of discomfort, and then remove the pressure/discomfort when the dog responds appropriately.
Many positive only and force free trainers will inform you that negative reinforcement is cruel because we are causing physical discomfort to the dog, when in fact, I consider training a dog that is in a frantic state, is emotionally unstable, and can't control its impulses, and using positive reinforcement, to be in many cases, abusive, as we are not being aware of the dogs current unhealthy psychological and/or physiological state during training.
Many cases I come across of dogs that are psychologically and/or physiologically unstable, are dog owners that have followed the positive only ideology from when their dog was a pup, and were not being fully aware of the pups psychological state when using a high value reward (such as food, toys, etc) to reward/reinforce appropriate behaviour. We need to be very aware of the power of classical conditioning when training, as we not only can create a conditioned physical response to a command or cue, but can also cause an involuntary unhealthy psychological and/or physiological state in the dog. This is particularly noticeable by me when I have observed puppy owners and trainers that use clicker training methods, that are more concerned with marking a particular response from the pup/dog, than being aware of underlying psychological and physiological states.
We train the dog in front of us. We never have a one method suits all mentality. Positive reinforcement is not always the most appropriate response when teaching a dog to do something, because as I alluded to above, we are always reinforcing more than just the physical response to a command or cue.