Around the tim Townshend was writing the album, a friend introduced him to the teachings of the Indian spiritual guru Meher Baba. So, when writing it, Townshed was inspired by some of the subject matter of his teachings. The two big ones were introspection and forgiveness. So, I think that that was a theme that came into play both in the original 1969 album and then the show as well. In fact, the only bit that was autobiographical was the song "Fiddle About," where Uncle Ernie sexually abuses Tommy.
Although the plot is more linear than say, The Who's second rock opera, Quadrophenia, Townshend has admitted in interviews that there has been room for people to view things in various ways. Do keep in mind, that, when Tommy saw in the mirror his mother's boyfriend being shot and killed by his father, he not only became deaf, dumb and blind, but also entered sort of a catatonic state that he snapped out of after his mother smashes the mirror. I think that it can be argued that because of him in that state, he may not have known what was going on between the torture being done to him by Cousin Kevin and the abuse by Uncle Ernie. That could make forgiveness easy for Tommy to do because he could have been in such a state where he was oblivious to anything happening around him.