My daughter will be 2 in January, and she is still breastfeeding full time too. She nurses throughout the day, and she wakes up a couple times per night and nurses - I can relate!! However, my daughter will take a sippy cup (she drinks water VERY rarely when I am home!) of pumped milk when I am away. The first time I left for a whole day, my mother had her (hubby deployed) and she took about 7 oz total that day (I left at 3 am, back at midnight for a work trip) - she was 8 months old and had never touched a bottle or a cup. Since then, she has had a few more days like that (3 total) and she has gotten better and better with the cup. Dispite the fact that normally I am available as needed to her.
I don't think you are stunting her growth - average age of weaning world wide is 3 years old, and the WHO recommends breast milk until age 2 at a minimum. So while americans are weird and therefore will claim you are damaging your child, remember that our society is unusual in our practices regarding nursing.
All of that aside, ditch the bottle. At your daughter's age, there is no need for it. Give her a sippy cup NOW (before wife leaves) with water in it, and continue BFing as usual. Then, when mama is away, she will already know how to operate the sippy cup, and you can offer her pumped milk or water or whatever your family feels is an appropriate beverage for her at this time. I also think that if you remain laid back, she will not be to worried about mama's absence. They are very out of sight, out of mind at this age. But if you are stressing, she will pick up on that.
Have fun with your little lady!