I'm happy that you have asked me to assist you with your child and hope that you can benefit from my many years of helping parents like you.
Let me see if I can offer some advice but not necessarily take sides:
First, to solve this problem the simplest solution would be to get her off the bottle since after a year of age no baby needs the bottle. Then you don't have to worry about contaminated milk.
Now, having probably scolded you enough, let me answer your question. Since you are using organic milk with no preservatives in it I would not re-use a bottle that she has taken sips out of simply because her germs are introduced into the bottle with the first suck and without the preservatives the bacteria can grow unimpeded, even in the refrigerator.
Again, since your wife is no longer nursing it is best to wean directly to cup, even a sippy cup, so that you don't have to wean again from the bottle. When you wean from the bottle or the breast infants and toddlers will necessarily drink less milk and that is fine for this age when they need to begin to have other calorie sources from a more rounded diet of veggies, meats, fruit, juices, etc. Don't worry about how much she drinks, which is the main reason parents hesitate to get rid of the bottle, as the milk calories are rightfully and quickly replaced with other foods, which is appropriate for her age anyway.
I know I've probably given you TMI but I can't help myself sometimes from throwing in some other advice that seems appropriate for the situation at the time.
I see you are offline still but if you have any questions please don't hesitate to ask.