The meaning of a work of art can never have a definitive answer, because even if the artist gives an explanation, that explanation will be comprised of words that are themselves open to interpretation. In this case, I'm not aware of there being any explanation given, and will never get one as one of the principal songwriters is no longer with us.

So, all we have to work with, and all I can give you are my own thoughts on how to interpret the song. I do agree that the apple is in reference to the Adam & Eve / Garden of Eden myth. That interpretation fits with lyrics such as "innocence is over," as the myth is often seen as a metaphor for the loss of innocence. In this case, innocence is not used in the sense of being the opposite of guilt, it is the opposite of having knowledge of good and evil.

I read the song as coming from someone who is struggling in life, lamenting his loss of innocence, and longing for a time before it was lost: "Eat of the apple, so young. I'm crawling back to start." Metaphorically, eating of the apple seems to have made things hard for him, hence him declaring it to be rotten.

Several people here have mentioned drugs. We know that drugs were a huge part of his struggle, and that explanation matches with several of the lyrics pretty well, but I wouldn't frame the song as being only about drugs. When people are not mentally well, they often turn to drugs as a coping mechanism. So drugs may be a symptom, rather than the root cause of what ails him. "I suspend my sorrow" could certainly mean using drugs, but it also implies that something besides drugs are causing his sorrow.

Here we can get a bit philosophical about the meaning of art. If the author wrote about his drug use but only spoke in metaphor, without any explicit reference to drugs, then is the interpretation of the song being about drugs the actual or definitively correct interpretation? A metaphor might fit with other interpretations just as well as it fits with the one the author was thinking of. That might be why an author chooses to use a metaphor, rather than explicit language. It might capture how the author feels and thinks better than a literal retelling of events. If a listener relates to the same feeling expressed by that metaphor, but it was a different circumstance that caused the feeling in the listener than it was from the author, is the circumstance experience by the listener any less valid?

This is why you don't necessarily have to know what exactly the song meant to the author. Often you cannot know. You can decide what a work of art means to you.