At this point, I'd say you need to choose your battle. Since she is on the low side of the weight spectrum and her health/nutrition is of good concern to you, I'd keep the bottle around for another 4-6 months. It doesn't hurt her at all, it doesn't increase the potential for cavities or long term orthodontic issues. The big concern would be her health at this point. Not getting the nutrients and fluids that she needs each day will cause more harm than the bottle.
My now 4.5 yo son was a paci sucker until he turned 4. We tried to take it away around age 16 months when EVERYONE else said it was time for it to go. Then I got preggo with DD and was put on bedrest. We were also potty training my son at the time because that's what everyone else said to do. We put both the paci removal and potty training on hold until after my DD was born and our schedule returned to normal. Then we decided to keep the paci and do the potty training when he turned 2.5 years old. It took my son about a year to be fully potty trained. That was a few months shy of his 4th birthday. So we told him that on his 4th birthday, the paci's would be given to the paci fairy to give to other little baby boys who needed them. He only asked for his paci for two days, then that was it. He also took a bottle until he was about 2 years old. He's got perfectly straight and very well spaced out teeth.
My 2.5 yo DD got off the bottle around 1.5 years because she wanted to drink like a Big Girl just like her brother. She was never a paci sucker, but is a FT thumb sucker from age 3 months. Her thumb and her blankies are her comfort items. She still gets a sippy cup of milk at bedtime. So far no cavity problems. But for sure she will need some ortho work as she gets older. She's got an overbite. Not sure if that's because of the thumbsucking or just genetics. Both my Mom and I were thumb suckers and didn't have to get braces. I do have braces on now, but my ortho said it wasn't because I sucked my thumb as a kid, it's because over time your bite changes. My SIL however needed braces as a kid because of a severe over bite, so we figure my DD gets it from hubby's side of the family since she generally takes after my hubby's side.
I also second the straw idea. Some kids just don't like the feel of the sippy cups...some spouts flow too slow/fast, some spouts are too hard or soft, and some just taste funny. My son loved the Platex hard spouts because he was an early teether and loved to gnaw his gums on it. My daughter hated them. The only sippy cups she liked were the soft spout Nuby ones. At about age 2 they both figured out how to use a straw so whenever possible I let them use a straw. I think with my daughter I must have bought every type of sippy cup out there before we found the Nuby ones. And they are the cheapest ones there are at only $1 or $2 a piece at Walmart :). Now she uses either a Thermos Sipster (LOVE these! They are expensive at $15 each, but they are practically indestructable! And hardly any leaks!)with straw when we are out and about or a Toss and Go sippy cup (again the cheapo ones from Walmart at about $3 for 4) at home.
What I have learned in my short life as a Mom is to always go with MY gut instinct with regards to raising my children. Just because 99% of the other Moms do things one way and it works for their kid, that doesn't mean it will work for me and my kids. Often times that meant I went against even what my ped recommended. You know your daughter best, so you are her best advocate and defender and instinctively know what is best for her. Trust your gut. If taking away the bottle right now is what you feel is right, then go for it. If you feel it's better for her to keep the bottle for a little or even a lot longer, do that.