I would agree that if Zion can withstand this attack, it will send the matrix into a loop, because look at what the architect said about Neo needing to put his code into the source. It may be that they have to sacrafice those in the matrix for all mankind to continue? Or maybe it is just Neo who will have to sacrafice himself?
What i believe is that there is two levels to the matrix structure
The first level is "the real world" and the second is "the matrix" as the people believe it is. i think the A.I have made the first level a real world to the people in it to make the people think they are free but acctually, everywhere u go ur in. also, they could have the first level to keep all the potential people that would resist the system in one place, so they can be easily exterminated when the time comes.But, as we all saw at the end of reloaded, Neo probably relized that he was still in the matrix and was able to use his "powers". In the third movie i believe that Neo will preach this fact to the people of zion and they will have thier supernatural abilities in the fight against the machines. since they would have these abilities they could probably defend zion. since Neo would know about the two levels of the matrix he could"move in and out of the matrix as he pleases" like the movie says.
If zion stands then the reloading process can not take place then Neo can become a threat to the real real world.now people can be freed fromthe entire matrix,and only then can it be fully destroyed.