In her new piece, investigative journalist Maureen Orth claims the actress was vetted by Church officials as a potential girlfriend for the movie star in 2004.
Orth alleges Boniadi was punished by church leaders when she breached confidentiality agreements and turned to friends for support when the relationship fell flat.
Scientology representatives have been quick to dismiss the article, but Haggis, who 'resigned' from the Church in 2009, has written to Showbiz411.com's Roger Friedman to back up the Vanity Fair story and defend his friend.
He writes, "I’m appalled that any church would treat its parishioners this way, but Naz has never cast herself as a victim. She is strong and resilient and I am very proud to call her a friend.
"Naz was embarrassed by her unwitting involvement in this incident and never wanted it to come out, so I kept silent.
"The last thing she wanted or needed is this kind of publicity, but here it is, and I am sure she will deal with it with the same grace and dignity she exudes in her daily life."
Haggis also reveals in his email that Boniadi "quietly and privately resigned from the church a couple of years ago after several years of trying to handle this injustice internally, to no avail."