Is she having several bm's every day? My son has always had issues with constipation and I think that since he's been on cow's milk, he poops almost every day, which is a good thing for us. Have you talked to your pediatrician about it?
As for the switch, you can always mix formula and milk, making the ratio of formula higher and then gradually switching it until she's drinking only milk. Try 6 oz. formula to 2 oz. milk at each meal for a week, then 4:4, then 2:6.
We also only give our son organic milk - it's better for him, for the cows and for the environment so I think it's a good choice.
Finally, I know some posters will tell you that your daughter does not need cow's milk to receive proper nutrition. I grew up on milk, need the calcium, and love its taste so that's what I choose for my family, but that's just another perspective.