Is she underweight, or is there a medical reason why you need to be overly concerned with her eating?
The reason I ask is that I've seen lots of moms get a bit fixated on their toddler's food consumption constantly concerned that they're not eating enough, or not good eaters, and this can turn into a disaster later in toddlerhood...where you've got a 2 year old using food as a hot button with mom...and it's not fostering healthy eating habits later in life.
Do you know her cries well enough to know if she is crying because she is sad/upset, or if she is crying because she is mad about not getting her way? I had a REALLY hard time distinguishing those cries when my DS first started to throw fits when not getting his way (which for us happened around 12/13 mos), but if you listen and assess the situation you might find that she's really just throwing a tantrum for the bottle. And that's the point that you have to decide what you'll give in to and what you won't.
I TOTALLY understand that you're concerned about her not being a good eater, but unless there's a medical reason that your Doctor is concerned with her weight gain, I'd say decide when she can and can not have a bottle (i.e. she gets one before her bath, and all other beverages are delivered in X type of cup) and stick to it (regardless of crying) and also decide when she can and can't have food - like establish snack times to sub for a bottle time. For 4 days. You might want to think about the typical times that she cries for a bottle too, and then try to avert the bottle cry by offering a snack before she gets a chance to realize she's hungry/thirsty and wants a bottle. Above all, I'd say figure out a plan and stick to it for at least 4 days before you decide something's not working.
((((((((((((((hugs)))))))))))))))))
I know it's frustrating!