Well let's take care of your pediatrician's fear about future orthodontics right now! Seriously, you hit the nail on the head when you talk of this as an unfortunate habit that needs to be broken. You don't say whether you have the same problem with putting your son down at night, so I'll comment on naptime techniques which can also be used for nighttime sleep as well.

As long as your son is well nourished and hydrated when he is going to nap, there should be no concern that the bottle contains any food his body needs at that time. So we can assume that this"treat" is clearly a sensory"extra "as well as a well established psychological,transitional object that signals his nap response.

First,let's be clear that the objective is to have him self-calm without his bottle. I would transition him gradually by giving him his last bottle feeding well before his nap. I would locate his favorite comfort object (blanket, safe bed toy, etc.) and make a big deal of going for a nap with it. I might also introduce some quiet, soothing music or a "sound machine" that makes the sounds of rainfall, a river, wind through the trees just before you put him down and keep it playing throughout his nap. When he screams for his bottle, as I expect he will, you can let him cry for about 5 minutes, then go in and pat him, talk soothingly to him for a few minutes and leave the room. Your second visit in response to continued crying should come after 10 minutes of crying, go in and do what you did before, encouraging him to go to sleep. Don't ever pick him up or stay there until he falls back asleep. The goal here is to let him learn to self-calm while he is awake in the crib. The third time and all successive times you go in to respond to crying will be after you let him re for 15 minutes. Add 5 minutes to each wait period over the next three days so by day three you'll be waiting 15 minutes before you check him the first time, 20 minutes before the second and 25 before the third and all subsequent checks.

I know as you hear him screaming it will be painful and you will feel guilty. Unfortunately, you have to take firm steps to reverse this habit and this means sticking to a plan. There are variations on this plan which you can play with. I guarantee you things will be better soon. Good luck.