So again, it appears there is a "controversy" only when one wants to look at verses like 1 Timothy 2, etc, in a way as to ignore it's prohibition on women in church authority. Otherwise, it's just fine to leave it as is. All we have is speculation.
Now, let us, for the sake of argument, say Junia was a female apostle. This does not mean she had authority in the church. Remember, Paul mentions her in conjunction with her husband, denoting her submission to him. If we look at the verses in the light of a woman who is submitting to her husband, then nothing changes. We have a woman, either as an apostle, or an apostle, who had a gift of ministry. Missionaries have the gift of ministry. Comforters of the sick and those who've recently lost loved ones, is a ministry in the church. Teaching children and other women, is a ministry in the church. Deacons (or deaconesses) have the ministry of helping within the church, yet hold no authority.
Now this all ignores that in Jewish culture at this time, women were always listed under their husbands in greetings, but that's a little beside the point right now. So you see, you've jumped to a conclusion not supported by the facts at hand. You assume that because she might be a female apostle, she somehow had authority in the church. However, now we must start ignoring the plain words of other scriptures, and must now start trying to twist them to fit the hermeneutic you've just invented, based on a current sociopolitical view.