Hi M.,
We started by switching to water in the bottle to help put our fears of rotting teeth to ease. I will admit we had the bottles thrown at us when we first did this, but we said it was water or nothing and then magically they (my twin boys) were fine with water. Warning: full diapers in the a.m.
Then we went cold turkey. When they were asleep we took the bottles out of the crib and then hid all evidence of them in a black garbage bag in the garage. When they awoke and wanted a bottle, we showed them that all the bottles were gone and that we didn't have any more. We offered a sippy cup, which wasn't pleasing to them. We set it in the bed with them but they never took it and after a couple days we quit giving it all together.
They did cry, but it only lasted a few nights and the first night was the worst.
My boys were around 20 months when we finally got rid of them. It's hard to do at this age, but completely worth the effort.
In terms of calories, I feel your pain. My boys were small and we had to work hard to get them onto the growth charts and up to the 50th percentile they are at now (almost 3). If your daughter doesn't like milk and you're worried about calories, the best thing to try would be an Ensure drink, or Boost, or something like that with calories and nutrients. Also, have you tried vanilla soy milk? She might like the flavor of that better. If you haven't had soy milk before, just know that not all brands are the same. They each taste different and you'd have to try around for a brand she'd like. I don't suggest chocolate because it can be too addicting at this age, but a vanilla might be ok.
Just my thoughts and my story. Good luck!