You are experiencing what many men find out about domestic violence cases -- it is impossible to prove that you did not lay your hands on your wife. This makes defense of these cases difficult because the history between the parties is usually ignored by the prosecuting attorney. If you want to fight the case, then you may have to set it for Trial to get to the bottom of if. This usually works to bring things to a head but there certainly is no guarantees. If you have to go through a trial then you rely on the Judge or Jury to apply common sense to determine if an assault occurred.
I would strongly advise you to consult with a criminal defense attorney who is not court appointed. If you have not been convicted of any crimes before then you may have other defense options available, too.
I have handled many domestic violence cases and could help you. If you would like to discuss your situation then just call my office. Thanks.