One might think this was a dead issue, but people keep bringing it up.
Why would anybody think Moiraine was BA? Well, during TGH, RJ seems to be putting down clues in that direction. Namely, she was missing during the time of the DFS. Also, she was wearing her ring on a different finger than she had before (damning evidence, for sure). This was all a red herring, because since then, we have been privy to Moiraine's thoughts, which show that she walks in the Light.