The award-winning director also said critics should perhaps direct their anger at those who ordered US torture policies instead.
The Oscar-nominated film opens by declaring it is based on first-hand accounts of actual events. But a senator and other lawmakers have criticised the movie as misleading for suggesting that torture led to bin Laden's location. Lawmakers asked Sony Pictures to attach a disclaimer that the film is fictional.
Kathryn wrote in the Los Angeles Times: "Experts disagree sharply on the facts and particulars of the intelligence hunt, and doubtlessly that debate will continue."
The filmmaker, who scooped an Oscar for her 2009 movie The Hurt Locker, continued: "As for what I personally believe, which has been the subject of inquiries, accusations and speculation, I think Osama bin Laden was found due to ingenious detective work.
"Torture was, however, as we all know, employed in the early years of the hunt. That doesn't mean it was the key to finding bin Laden. It means it is a part of the story we couldn't ignore."
She added: "War, obviously, isn't pretty, and we were not interested in portraying this military action as free of moral consequences."
Kathryn and Zero Dark Thirty screenwriter Mark Boal had said previously that they depicted a variety of controversial practices and intelligence methods that were used in the name of finding bin Laden.
"The film shows that no single method was necessarily responsible for solving the manhunt, nor can any single scene taken in isolation fairly capture the totality of efforts the film dramatises," they said.