In Matrix Reloaded, the Architect explains how Zion was part of their plan for the 1% of the population that reject the Matrix, but he doesn't explain WHY the machines created Zion in the first place. Why couldn't they immediately kill the 1% so that they would save the trouble of having to deal with them later on? If the humans are unplugged they are obviously useless, so why keep them around?
Zion wasn't just a refugee camp, it was also an armed base sending soldiers into the Matrix to locate new recruits. Ironically (and unbeknownst to the Zionese), they were actually helping the Machines by using their skill and cunning to locate, remove and then contain potential troublemakers in one place.
Once the numbers in Zion have reached a critical level (e.g. where the inhabitants are starting to think about spreading beyond the limits of the city and fomenting genuine unrest within the Matrix) the machines then step in, kill almost everyone and restart the process.
Beyond the obvious, Zion serves four main purposes;
The way I understood it was that Zion was something like a pressure valve.
The Architect knew that his equations will always produce a few dissenting humans within the population. These dissenters could destabilize the whole Matrix and bring it crashing down. The equations said that he could never completely get rid of them. So the next best thing to do was to contain them. Give them all a place to call home. So instead of each group of dissenters creating their own pocket of resistance, all of them are now under one umbrella group: Zion. Having all the dissenters in one place means that you can watch them and monitor them. Keep up the illusion that they are completely independent, and they will continue to grow their central city and not venture to split up. And if the humans become too troublesome, well the Machines already know that they are in one place, and it's just a matter of exterminating them all.
I believe that Zion is just another level inside the Matrix. The Machines gave these people the illusion that they are (now) in control of their own body in Zion. But in actuality they are still plugged into the Matrix and are still being harvested of their powers (bioelectricity) so they are not actually useless.
tl;dr: In my view the main purpose of Zion, from the viewpoint expressed prominently by the Architect, is not to collect the rebels but to keep the Matrix functional at all.
At least two initial iterations designed by the Architect were disfunctional. Zion must have been systematically introduced when another program, believed to be the Oracle, provided an unsystematic but functional solution to keep it going.
Since without Zion the whole Matrix fails, its single main purpose is probably to allow the Matrix to remain in working order for extended periods of time.
proof tl;dr: if the rebels were truly use-less or an unorganized threat to the Machines, the Machines would instantly kill them because it is them unplugging the humans from the power-plant, with this robot:
Since the Machines, at least the Architect-"branch" of them, are associated with efficiency and systematicity, the reason they don't kill the awakened humans at this point is most likely because they don't want to.
That rules out all four of Richard's proposed main purposes, because:
If the rebels were useless, they would be killed, there would be no system crash inflicted by them, so gathering them in one place for a long time just for a supposedly "easier" kill-off and to ensure system-crash handling doesn't make sense. Then of course if they weren't exist at all, they could not attack the Machine City, and they couldn't recruit the One either. Thus all four points are ruled out.
The movie-fact that may mention an actual reason for the Machines to allow Zion, is that we've been told the Matrix was needed to be re-designed based on an other solution, believed to be found by the Oracle, which then most plausably contained Zion.
I originally had a very long analysis but I decided to remove it. Will share with anyone interested. I tried to make the points in the short versions above. However it also contained passages trying to point out several perceived assumptions in your questions. I re-mention these assumptions:
One assumption is that Zion should be initially machine-built which may be wrong, because the Architect only says that they have destroyed it six times, and that "individuals" will be required to be selected in order to rebuild it.
The other assumption which may be the more flawed is that ther rebels should be deemed "useless" (supposedly by the Machines). They are not becuase if they were then the Machines would kill them when they awake.
There is another remotely connected assumption, that there should be no other forms of intelligence on the planet (supposing there is a planet) but the Machines and the Humans; however, the Machines are mainly associated with Agents, Sentinels, Machine City and the Architect. But the Architect does not exercise control over the Exiles. It is known that they can get things out of the Matrix, so they can live outside it. They behave clearly very distinctively from other machines, the Agents wants to kill them more than the rebels, and they are handled separately in the franchise's supposed canonical continuation The Matrix Online. They can be a third "form"; even more lifeforms are not mentioned although not ruled out either.