I think the Smith exploding thing is kind of a bookend for the film. The first and last ended with Smith exploding, but Reloaded didn't. I think, symbolically, Smith (or any program) that seems to explode means it's being absorbed by the source... thus the bright light. Remember, to Neo, the entire machine world was made up of lights and the door leading to the source in Reloaded was a bright, white light, too.
Yeah, I could tell by the look on his face after Trinity died that Neo was probably planning on sacrificing himself. He remembered that the Oracle told him that the only way to reach the future was "together," meaning by working
with the machines. Pretty sure I mentioned in one of the Reloaded threads that Smith was the only variable that had to be contained in order for humanity and machine to have peace again... or something like that.
I'm glad they didn't go "formula" and kill Locke. He's easy to dislike, but he was right about that EMP, wasn't he?
Besides, would you really want an idealist like Morpheus in charge of Zion defenses? I wouldn't. I'd pick the pragmatic a$$hole anyday, 'cause I'd know that I could count on him to do his job in spite of his "beliefs."
Morpheus is good at what he does, so he should keep doing it. There will be others to free, still, and the Architect promised not to interfere.