- He wouldn't want to.
- He can't anyways.
Disabling The Black Zero Means More Powered Kryptonians
If he didn't want to kill Zod outright it was within his abilities to leave him on an inoperable ship in permanent Earth orbit where the threat to his son and adopted planet was nullified.
This would be a disastrous plan, inviting many more solar-charged super-powered Kryptonians into the fray.
Please recall that the Black Zero is equipped with Drop Ships and Escape Pods which are all capable of making earth fall independent of the operation of the ship. A Drop Ship initially picked up Superman and Lois. A Drop Ship then allow Zod and Faora descend onto the Kent Farm. A Drop Ship rescues Zod during his sensory attack and withdraws Faora once she's out. A Drop Ship takes Zod to the Scout Ship in the Arctic. The Drop Ships are capable of taking out A-10 and dropping Superman. Meanwhile, the Escape Pods- when not punched by a Kryptonian- are capable of bringing Lois to Kansas and getting Faora from the Black Zero to the C-17 mid-flight.
On the ship, shielded from radiation as all spaceships are, the Kryptonians are powerless and vulnerable. Which is why Lois can stop them with small arms and why they're blocked by conventional doorways dropped by AI Jor-El. On the ship, they're close to the Phantom Drive which is Jor-El's plan for banishing them.
Even if Jor-El could, hypothetically, disable the Black Zero, all that does is compel the Kryptonians to descend onto Earth en masse from Drop Ships making multiple rounds and Escape Pods capable of getting them Earthside. Then soak up the Sun and now humanity is facing an infestation of Superman-level threats. Bad idea.
Aside: Zod acts as a check against more powered Kryptonians because he doesn't trust everyone one his ship. If Zod believed everyone on the ship was 100% loyal, there was no reason to fight from space. Simply deploy all the Kryptonians at once and receive the exponential multiplication of force. However, Zod's ultimate goal isn't power, which he could acquire setting up under any yellow sun. Zod's biologically programmed purpose was the reconstitution of Krypton just as it was before. NOT a superhuman collective of democratized supernatural powers across the population BUT a society ruled by caste, class, and codes. If all the Kryptonians are powered the only thing keeping them in check is their loyalty. If New Krypton has normal Kryptonians, then rule is run by the Codex, councils, bloodlines, and military might.
Why would Zod fear disloyalty?
First, he himself is a betrayer. Bred to be loyal he's the head of a coup d'etat. He'd have personal knowledge of the possibility if not outright paranoia of facing the same. This is why only his most loyal lieutenants are allowed Earthside and why Zod, himself goes. Only THEY can be trusted to taste the fruit of supernatural power and resist the temptation to cling to it over Krypton's resurrection. Normally a general leads from the rear and sends foot soldiers to do his bidding. Zod doesn't do that because they can't be trusted to enjoy godlike powers and give them up for the cause.
Second, there's a good chance that not everyone on the Black Zero are Sword of Rao or Zod Loyalists. You pointed it out yourself: Jor-El designed the prison ship before Zod's surprise rebellion during an energy crisis that was anti-space travel. It HAS to be before because Jor-El dies during Zod's rebellion attempt. The ship wasn't a response to the rebellion. So if your society is desperate for resources and hates space why do you build an orbiting prison? The answer is obvious: because you need to... because you have convicts to imprison. Prisoners convicted of their crimes before Zod's coup and not because of it. That means there were prisoners on the ship BEFORE Zod's coup and not a part of Zod's coup... prisoners that wouldn't necessarily be loyal to Zod if given Superman-level powers if the Black Zero disembarked on Earth.
AI Jor-El Is An Exploit Not Omnipotent
He tells Kal-El he can save Lois and humanity, so why not ensure it with a snap of his fingers?
Which analysis is consistent: Jor-El acts within his ability to enact his stated intentions and desires... or Jor-El says one thing but does nothing to effectuate it?
Your contradiction and objection arises only if AI Jor-El has the ability to end the Kryptonians with a thought. It's obvious that he doesn't. Jor-El could not directly release the bonds holding Kal-El. Jor-El couldn't keep Zod locked in a mental simulation or worse. Jor-El couldn't eject the pods, throw the ship into the Sun, sic the ship's defenses on them, blind them with holographic projection, or do anything damaging. Why? He's a hack and an exploit not an omnipotent god.
As an invasive AI on the Scout Ship, Zod is able to dispel AI Jor-El with but a word and the push of a button. And that's AI Jor-El on a ship 20,000 years old, say nothing of sophisticated systems Jor-El himself designed millennia later. Sentient AI is new but not totally unthinkable to Zod (he isn't blown away by its existence but still has questions about it's parameters: does it feel pain?). It's likely that in a society steeped in AI, they've already engineered the safeguards that prevent AI from rampancy or violent disaster. Either as a limitation of AI themselves or in systems that refuse their control. [Ex: You NEVER let AI jump you into a star.]
So what powers does AI Jor-El have? Doors and atmospherics. That's pretty consistent with a fire-suppression system and AI driven safety. You alter atmospherics to kill flames and you control doors to cordon off the spread. AI Jor-El's powers on the Black Zero don't go beyond that because:
"Ship, have you managed to quarantine this invasive intelligence? Then terminate it."
AI Jor-El is an Internet-of-Things attack on your Thermostat... not demonic possession of Amityville.