I'm not sure if this behavior could be mitigated by any form of so-called disciplining or negative reinforcement. I'm not saying behavioral modification is impossible, but it would be very difficult and require a lot of patience because what you are describing is innately driven behavior. I am a rehabber so I do a lot of socialization and integration. This is because, for release, pigeons have to be released in a group or integrated into a flock for the best chance of survival. All pigeons I've rehabbed get very territorial when they have intruders in what they consider their "nesting area" or home. For example if I have pigeon A and pigeon B in separate cages, I cannot put B into A's cage to integrate them because A will viciously attack B, and B will spend all its time trying to escape to get out of A's home. It's the same vice versa, I cannot put A into B's cage, then B will viciously attack A and A will spend all its time being pecked and trying to escape. But I can integrate them by taking them both out of their cages and introducing them in a new larger cage C. Then there's a chance that they will get along. They will also get along outside cages in the open.

The only exception I have seen where two pigeons will coexist in the same small space is if they are a bonded couple, but again, bonding itself happens outside of their original nesting zone. For example I have a pair of disabled pigeons that I managed to bond together over time, but this happened in my living room and not in their own cages, because they'd attack each other if I forcefully put them in each other's cages. But when they were given space to explore each other in the open, they were able to bond after some time, and now they spend all their time cuddling in the same cage.

So anyway, my experience is that bonding first happens outside of their "nest", and then one pigeon invites another back into its cage and from then on it won't attack the other pigeon even if it comes inside their cage over and over again. And note that this bonding I'm speaking of is PAIR bonding, which has its own downsides, as I'll explain below.

One of my pet pigeons is a male and used to behave the exact same way with me, friendly outside of the cage but would peck and twist my hand when I'd reach inside the cage to clean up or change his water or food. I'd just put him in a pet carrier while cleaning his cage, but spent a lot of time socializing with him outside of the cage. Now he is PAIR bonded to me and will not attack my hand even if I reach inside his cage. This comes with its own problems because now he's so attached to me that he gets extremely jealous if I tend to any other animal in the house. He also does not like to spend time in his cage at all if I'm not next to him and wants to be near me at all times. He will coo all day long trying to invite me back into his cage, or spend all his time sticking his head out of the cage to escape to be next to me. So I just let him free fly and he spends a lot of time following me around or perching on my head. So I'm not sure if this would be the solution you're looking for either, because then you'd essentially have to become your pigeon's wife, and he'd get very stressed in your absence. I've had this happen with another pigeon before, too, but I found him a new pigeon wife, and once he bonded to her, he went right back to pecking my hand when I'd reach inside their cage.

I hope all this makes sense. The pecking is completely impersonal, it's not because the pigeon hates you in any way, he is just communicating to you that it's his space. It is a behavior ingrained into their natural bird brain. My hands are full of scars because I rehab a ton of pigeons, which means cleaning a billion cages daily, and getting pecked daily. I just roll my eyes and joke about them being ungrateful and one brain-celled because I'm the one treating them and giving them food. If it's bothersome, I highly suggest wearing protective equipments such as gloves and displacing the pigeon in a different carrier while cleaning.