I know I'm just mirroring your confidence here, but you're absolutely wrong in this respect. The dinosaurs do NOT represent nature. Like Frankenstein's monster, they are the outcome of man's attempt to play god, and as such are a flawed imitation of nature. Ian Malcolm is meant to be the voice of reason (and voice of the author) across the two books. It's why Crichton brought him back for the sequel when his death pretty much assured at the end of the first book.
"Malcolm came back because I needed him. I could do without the others, but not him because he is the 'ironic commentator' on the action. He keeps telling us why it will go bad. And I had to have him back again."
One of the things that I do really like about the JW movies is that Wu does make a point of explaining that he didn't really create any dinosaurs to begin with. They're all genetic hybrids and designed mostly along the lines of how people expected them to look rather than how they might have looked naturally. The original did touch upon the DNA gap filling, but Wu's scene with Masrani drives that home.
The dinosaurs aren't nature, but the point is that life finds a way to break through the barriers that man puts up to control the world around them. And it's not just in the whole breeding secretly part, the storm in the first book/movie is also a force of nature that man ends up ill-equipped to deal with. Yes, Nedry and the corporate espionage plot line is also part of the catalyst, but even his best laid plans falls victim to the forces of nature (the storm).
In JW2, the volcanic eruption is also a force of nature the characters must contend with, but it doesn't have that same impact. In the end, all the good guys survive and the goal of saving the man-made dinosaurs from the natural order is more or less achieved (even if it's the bad guys in control).