An interesting topic! Certainly there's no consensus on what really happened, as the only evidence lies in Darius' inscriptions and the Greek versions of the story, both ultimately derived from the same 'official' accounts of what happened. Personally I would like to think Darius' account was true. There's also the fact that he gained legitimacy by marrying Atossa; I would find hard to believe she wouldn't have opposed him had he murdered his brothers.
This article may interest you, it deals with the details of what is known.