You don't get it.
We're already in a "conflict;" more than that, we're in a war. We have no access to any such resources.
Maybe you don't understand this because you're on the other side and you've never had to worry about being killed by them in either the Real or the Matrix. But for us, it doesn't get any worse than it is right now.
I realize that without the Matrix, there is no purpose for Merovingian operatives and Cypherites. I realize that without the Machines, there is no purpose for Machinists, and no war for E Pluribus Neo to fight. Only the unified cause of humanity would remain. The cause of living the best life possible. The cause of making the best of the environment and founding a society. Would there be struggle? Sure. If there is not one struggle, there is another. I believe any struggle that might result from a human conflict would be on much lower scale than the battle we are locked into against our will right now. In any human conflict there is, at least, room for discussion.
I am not so fatalistic as you - that is, I do not believe in human nature, or any form of determinism when it comes to the thoughts or actions of man. Perhaps you have been a Machinist operative for too long, and have come to associate the behaviors of the machines, those that are formed through absolute logic, the result of thousands of subroutines compounding variables through mathematical equations coming to one, and only one possible outcome, with the behaviors of man.
I do not believe in "human nature" - it implies that we are without a choice in our behaviors, and that we have no responsibility for our actions. Truly, if you do believe in "human nature," you must concede that we could not help but create New Zion. It was the only course of action our "human nature" would allow.
But moreover, the presence of at least five clear subdivisions among human alignments in this war proves the impotence of "human nature" - after all, if human nature existed, we would all act as one hive mind on one side, and there would be no more than one human organization.
There is always a choice. At least, among humanity. We need only make it to the point where we may make that choice.
As you say "you will destroy yourselves," I say we will have the choice. As I say "they will destroy us," I know that this is an absolute.
I would rather have the option to die than have it forced upon me.