Let me start off by saying I have no children. That being said, I see no problems with the OP using a harness to keep her children safe. And yes, that it why she is using them. Let's put a few of the other examples you used into perspective.
1. Prisoners -- besides the fact that it's laughable to compare the OP's situation to a prisoner, they most certainly do use restrictive devices in prisons. All the time.
2. Elderly dementia patients -- They typically cannot RUN away, and there are certainly plenty of "restrictive" devices that people use to keep them safe; they just may not be as visible as a harness. A wheelchair is often used so they don't wander. My dad had dementia and before he passed last December, my mom put child locks on the bedroom door handle because my dad would wander, and we didn't want him getting out of the house. I live with them (her, now) and my mom could open the door in an emergency, and I could have opened it from the outside. We did it to keep my dad safe and so my mom wouldn't worry.
3. Children are still learning. They do not have all the rights an adult has, and so it is reasonable to have restrictions for children that we do not have for adults.
4. I have no children of my own but I absolutely would not hesitate to use a harness on any children I may have, whether or not they have a disability. I have some physical restrictions that are not readily apparent. I simply could not chase after a run away child. And if I had a child that never ran away, I wouldn't use it. But if I had a child who didn't listen and I knew would run if they disagreed with me then yes, I'd use it. So perhaps that is "punishment" but I see it as keeping a child safe.
To take the OP out of this and to make it a hypothetical situation, what would you recommend for someone who may be in a situation similar to the one I mentioned above? Would you recommend I never let the child out of a stroller? Would you recommend I never go anywhere with them alone? Would you recommend I use a harness all the time so it's not seen as "punishment?" Or, the other extreme, would you suggest I never try to restrain ("punish") them,if they run away? I'm genuinely curious as to what you would suggest, because I may have children one day and would like to avoid using a harness, but I see it as an almost inevitable solution in certain situations.