The ending gives the player two different versions of events to choose from, but realistically both the twins' account and Tom's version of events have logical reasons to call their stories into question. Both rely on partial information from biased sources that were lacking full context, trying to remember something that happened a decade ago. Most likely what actually happened was somewhere in between, with details misinterpreted or misremembered by both sides. It's not so much which one is true as which version is closer to the truth.
The version of Mary Ann's death remembered by Alison and Tyler was a traumatic experience which happened very quickly, both factors that could impede a person's ability to remember clearly. They were also both children at the time, and lacked a clear understanding of what was happening. Their resentment towards Mary Ann may also have impacted their views on how she was acting.
Tom's account has him watching from a distance at night, meaning it would have been hard to clearly see what was happening or hear what was being said, and it could easily have been misinterpreted. We also know that he may be trying to frame the story to make himself seem more sympathetic, and his obvious bias may have colored his interpretation of what was happening.
An unspoken option for what happened the night of Mary-Ann's death can be found with a little pondering: when Tom came to the dock in the middle of the night, Mary-Ann greeted him with a death threat and the shotgun. The night of her death, she was carrying the shotgun, and we see that Tom was lurking in the shadows around the property. It's possible that she had determined that he was around and gone to get the shotgun to make good on her threat, especially with the very good chance that CPS would take the twins away (he had said that she would probably lose custody to him if their parentage was ever discovered), but the situation spiraled out of control and ended in her death.
