What is most important is that your baby is consistently getting approx. 20 ounces of dairy per day (depending on age) for calcium intake. I'm surprised your doc recommended chocolate milk, why add sugar to the diet?? As others have mentioned, calcium can be obtained in yogurt, cheeses, and mixing milk into oatmeal for example.
I have twins and when switching from formula to whole milk, one loved it while one took his time. I kept at it filling up the bottle and only giving him that to drink. After two days, he reluctantly started to drink and then slurped it down with no issues. Had the same problem switching from bottles to sippy cups, again my perseverance (as difficult as it was) won out and no more drinking issues.
I think it's important to use whole milk (or another form of it like soy or rice) with more fat in it as your baby needs healthy fats now. Of course, your doctor should clarify this but that's what my doctor said.
Good luck!