AFWAW, I had this long reply out to you and erased it...you are doing well. Do not let your emotions control your actions without thinking it through...sometimes it is okay to get angry.
If your wife continues to put your daughter in the middle you need to talk to your wife.
Your daughter is old enough to know the truth and probably already knows more than you. She was with her while you were in Iraq.
If the affair is over then the reason your W comes back matters not...if it is still going on to include her seeing these OM daily at work you are going to continue to have problems.
If you can get evidence, expose.and end this affair you can get on to working on your marriage. I do not want to see you slip into the "status quo" and continue like this for months/years and turn down a stripe or a good civilian job in the hope that you will get back together.
I do not think it is time for divorce but there is nothing wrong for you to prepare yourself legally. No matter what the outcome is you can do no wrong in paying off as much joint debt as you can. If she is still paying bills you had and her apartment (unless OM is giving her money?) then she has to be using savings or credit cards. Again, hope for the best and prepare for the storm. Her moving out and leaving your daughter is not going to look good...make sure you journal the conversations...handwritten is best. Leave it at work in your desk or locker. Do not leave it at home for her to accidentally find.
...take care of your daughter and watch her close. She should not be in the position of asking her mother to come home. How is she doing at school? A drop in grades and loss of interest in after school activites will be a good indicator for you that she is getting overwhelmed. Take care