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SPOILERS AHEAD
It's obvious that the corporation is relying more on the AI than on the clones. In a conversation they blame the AI for losing a worker and a digging machine on the same day.
Considering the level of technology it should be trivial to build machines to replace the clones, remotely controlled by the powerful AI. And if something went terribly wrong with the AI, the corporation already has a protocol to send a human team.
So why are there any humans at all in the lunar base?
Perhaps the point of the cloned humans is not really to assist in the mining but to test out the technology required to create them. The rapid deterioration of the clones on the base shows that this technology has not been perfected but it would be of huge use to a corporation involved in space exploration or industry.
The secrecy of the operation, maintained by the communication blocking devices on the Moon, along with the uproar caused at the end of the film by the revealing of the clone's existence suggests that such research would have been extremely vigorously opposed on Earth. However, an off planet mining facility is the perfect place to carry out such unethical research since access can be easily monitored and controlled.
I believe the company had to have humans to run the various equipment cheaply and to maintain the machines.
Basically the clones were the organic component in a closed system. While conceivably a moon base could be fully automated, one can presume in the Moon universe it's probably cheaper to use a dispensable human clone instead of only using mechanical parts which have to be built, sent to the moon and then replaced.
A clone could be grown or stored onsite and then injected with the correct memories. I think the idea behind Moon is that it was simply easier to use clones of the main character than to replace the human component with expensive parts.
I once worked as a manager/technician in a factory that had both advanced robotics and low-paid manual labor. The robots were much faster, but the maintenance costs in many cases were above what it would cost to pay 6-10 minimum to low wage workers. So some production lines got machines and others got humans. It's the same reason a lot of robotic capable work is outsourced to the third world.
Humans are cheaper to use than robots in many cases.
From Ebert's review of the film:
The station is largely automated; it processes lunar rock to extract Helium-3, used to provide Earth with pollution-free power from nuclear fusion. My guess is, the station is on the far side because you don't want to go gazing at the Woman in the Moon some night and see a big zit on her nose.
The station is large and well-appointed, has entertainment resources and adequate supplies. Sam communicates frequently with the home office ... and so does Gerty. Sam doesn't do any actual mining, but his human hands and brain are needed for repairs, maintenance and inspection.
I don't think that it's "trivial" to replace a human being. That said, in many ways, Sam's replacement clones are bioroids, programmable machines with a three year shelf-life with all the knowledge, adaptability, and experience of a Lunar Systems' engineer.
I would see the answer as being much deeper than one would first think. At this point and especially in this terrain and situation one simply cannot exist without the other. Clone or not, Humans have the ability to think illogically when its needed to do so, you only need to look at other classic science fiction examples to see. It intrigues Q on Star Trek, its defeated the Borg, etc. In the movie Moon also Humans have the ability to make self sacrifice for something illogical, love, or try to escape to earth even though they know in reality the child they wish to see.... Is not TRULY theirs, because they are a copy. If you watch the movie the martian, the survival instincts humans have are uncanny at times. With that in mind it can give them skills they may not even know they have. Machines are made for tasks.... As is shown on Moon, The AI Gurdy is fairly advanced but it takes a human to make it question a rule 'the room is out of bounds to awoken clones' Sam states 'if we do not awake a clone me and the other sam will die, do you want us to die'. Sam used a logical approach in a humane way an AI would understand, making the 2 work harmoniously, and it worked. Another machine may have just said.....i require door access, not understanding of course the need why. For the tasks themselves regarding work and mining, The AI is perfectly capable of course for the every day situation... But since when is every day without incident? Event on a remote mining landscape.... There needs to be the ability to think outside the box. Its not always about percentages its about importance.... Think of I ROBOT and Will Smiths anger at the robot who saved him in the car wreck, soley because he had the highest percentage rate of survival than a little girl that ANY rescue fireman would have saved first.... Which led to her not making it.... Machines simply dont take the illogical risk when needed... To a machine, thats completely baffling 'Why' is a big deal for humans, not often understood by computers. There will always be a balance requirement for man and machine
