Hi V.,
Just my 2 cents. When we weaned my son off of formula, found out he was allergic to cow's milk. So we had to go back, however we did do the soy milk and all was well. I just began giving him 1/2 formula and 1/2 soy milk for a few days and then 3/4 of soy and 1/4 formula, I think weaning it this way is better. On the other hand how important is it if she drinks it out of a cup or a bottle? She is about to be just 1 and still a baby, so a bottle is fine in my eyes. With my son, I could not force him to make the transition from bottle to sippy cup, he did that all on his own and each child is different. He gave me his pacifier, his bottle, and other various items that he no longer uses/does, but at his own time and pace. Some kids are better at this than others and that is what worked with mine.
I think as long as she is getting her nutrients, that is fine. My son is a strong, healthy 45 lbs. 42 inch tall big 3 year old boy and after the soy phase, he really doesn't consume milk anymore. He is still allergic to the cow's milk and he doesn't like the taste of soy and so he just doesn't drink any milk. As long as he is getting the sufficient amount of calcium, I wouldn't worry about it. My son loves, yogurt, danimals, cheese and so forth, so he is fine. We are NOT big milk drinkers anyway, so...maybe that is why. He does drink juices, (100%) that I always water down and have since he first began drinking juice, he is a healthy boy. 1/2 water and 1/2 juice.
Good Luck!
G. B.