He can't. But there's the rub.
The way you've framed your question it is implied though that he does in fact realize his self is contained within the Matrix (or that reality is not as his senses tell him it is). He has come to understand that all is not as he thought it was with reality. He has evidence of this- the incident with the Agents where they make his mouth disappear.
So, given that, what choices does he really have?
He can either:
Essentially "Live Free or Die". The "A" choice is explored in the movie by the choice that the character Cypher makes. He knows the Matrix isn't reality yet he decides it is better to be inserted into the perfect lucid dream (provided he is oblivious to this fact) rather than live an austere existence in what may or may not be the "real reality"- albeit one where he has at least some choice/control.
We face choices like this in everyday life. What is better? To live in a free society with no guarantees or to live in a Marxist "utopia" where all is provided but where you have no personal autonomy? Same type of choice. People answer this question differently. It isn't a given that people will choose freedom- to the contrary, it seems to me it most people would choose blissful peace, security and ignorance rather than be free and have to face Life's hard realities themselves.
As far as the "The bong-hit, dorm-room-bull-session "philosophy" behind the story"... Hmmm. This is a standard philosophical question that one would encounter in studying philosophy. It is something that has been pondered over for centuries. How do we know existence as we know it exists? The film, "The Matrix", is simply the "Brain in the Vat" question in a form that can be consumed by the masses. What is the harm in this? Why should philosophy be a dry subject or one that is seen as something you go off to university to study? Socrates discussed philosophy right in the street. If people find it thought provoking, this is a good thing. Philosophy shouldn't be locked up in an ivory tower. Why not have kung fu and philosophy on the same plate? Why shouldn't we have a little fun with these things?
There are parallels with the Matrix in our life though. Consider Operation Iraqi Freedom and the subsequent shock the Arab world suffered when they realized their perceived "reality" did not even resemble the truth. They have been fed Islamic dogma for ages. They have no free media. They truly believed the Iraqi Information Minister when he got on television and lied to them. They wanted to believe it. It is easier to accept that what you've spent your whole life knowing is the way it is rather than find out the entire spectrum of your society has been an elaborate and systematic fantasy world.
This is what many in the Arab world are dealing with (actually, it's something the world at large is dealing with at the moment- the unrealized gulf of disparity between the power of the US and other nations). I can sympathize with how they must feel to a certain degree. Imagine that the foundation that all your thoughts, all your beliefs, all your values rested upon was suddenly exposed as a fraud? There is no Arab military might. Cultural "fierceness" and an extreme willingness to die are no match what so ever for your enemy whom you perceived to be too weak and corrupt to triumph. Suddenly, you learn that compared to your own "reality" the Americans are practically god-like. They can do what they want, when they want and there's absolutely nothing you can do about it- and furthermore, adhering to your cultural perspective will simply increase this disparity and make you weaker. Not a nice situation in which to find one's self.
Where do they go from there? Interesting question. Not really germane to the thread but their world had been a fabrication that had been pulled over their eyes to hide the truth from them. They had never lived in a world where questioning the reality of their existence was allowed. Better, I think, to live in a world where totally awful films like the Matrix are out there for free people to choose to consume or not (to ponder over bong hits or not) rather than live in a world where only the accepted version of the truth is all that's on offer. That's really what the movie boils down to. Not so much "Is the Matrix real or not but "What choices would you make if..." It's all about choice.
That's just me though...