»Why did the Merovingian try to kill Neo?«

If the code can be successfully extracted from the One's dead RSI, then there is no need for the One to make a decision that effectively undoes all the "wrong" decisions made by the 1%. While there is no overt proof that this is what occurs when the One returns to the Source, I feel that this is the very thing that is necessary before the Architect can reload the Matrix.

Think about it. The Architect at least knew that Neo was the One by the end of M1 (or much earlier, depending on your opinion of how the One came about in the first place). He could then easily kill him the next time he's in the Matrix. The Architect, as the chief programmer of the Matrix, could do almost anything--even something as simple as having hundreds of blades appear out of nowhere and slice up the One's RSI into little bits. I mean, the options are limitless. If the Architect really wanted to kill Neo, he could, and in a very efficient manner as well. Even if it took something monumental that was visible by the entire populace, it wouldn't matter because the resulting reload would wipe that memory from their minds. No, Neo MUST make it to the Architect's chamber to make a choice on behalf of all the 1% who rejected the Matrix.

Neo could have balanced the equation like the previous five Ones by going through the right door. But by rejecting the Matrix, the problem of the anomaly continued. There was a price to pay for that. A choice to accept the Matrix still had to be made for it to continue to exist and for humanity to be saved. One way or another, someone had to die. Either Zion had to die, or the One had to die. In order to save Zion, Neo died in their place.

When Neo entered the Matrix for the last time, he was not aware that he would have to die to defeat Smith, but when he heard the words of the Oracle, he had his final bit of enlightenment. To save Zion and the rest of humanity, he was going to have to give up. Though it sounds like an oxymoron, Neo chose to accept destiny.

I know this might sound odd, but given the record of "the One" you have to give it merit. Maybe the architect is unable to kill the one despite his position and his tools in the matrix. The key to this for me, is the link between the One, and the source. He is trying to kill Neo in a world that is powered by the same thing that is empowering Neo. Hundreds of Bullet's stop, agents can't keep up, nothing can keep up... in fact... the system did invent a way to eliminate the One... and that is Smith. And Smith... ended up being a far greater threat to the whole world, then Neo ever represented to the machines and the matrix. And guess what... Smith in a round about kind of way, does kill Neo... and the matrix didn't crash.

Then their is the other simple truth... the machines (architect) are trying to eliminate choice, to solve it, not to allow it, or worse, empower it. Although the Oracle secretly kind of is... but she is not in the same boat as most of the machines... at least that's my own opinion and kind of besides the point here.

You can't put things in a vaccuum... If Neo complies with the architect, Smith wins... and he destroys everything. Talk about a price to pay... the anomaly has indeed become systemic. In the end, Neo didn't choose to accept the matrix, he chose to save sentient life on this planet. It's not Zion or Neo, it's just Neo... if Neo fails... Zion fails... everything fails.