Have you had her checked for thrush in the mouth? This can cause pain while feeding. Also, you could be on the right track about the ear infections. I have had a few ear infections this year, and if drinking from a bottle of water, it does hurt. The pain is very very sharp and searing, and even causes me to cry out sometimes.
Have you tried giving babys' painkiller, like Calpol? If this continues, please see a doctor or health professional. Feeding times can be a lovely time, its a shame if its causing upset for you both