Gesang,
I believe that I possess some alternative opinions on this one regarding your choice to breed her and the ethical views you have been given contrary to the decision that you made.
All IMMHO. There is no body of work regarding the breeding of injured/damaged chameleons and the effects such might have on offspring. However, we have plenty of such evidence regarding humans. We know that many debilitating injuries and conditions do not render a human female incapable of producing healthy and normal children.
It is true that while humans can have their every need monitored during a problem pregnancy, chameleons cannot. However, we are unable to provide such monitoring for the 50% of gestations in healthy chameleons that do not work out, so I do not see that argument as having merit here.
There is no evidence that she had genetic impairments. By all accounts you have full control over her diet, just as you would in preparing an otherwise normal chameleon as you prepared to breed her. We have no evidence that she was hindered by her condition in that preparation.
With the lack of success many have in breeding what they believe are healthy chameleons, to include the hatching of weak offspring, that never stopped the community at large from trying. Nothing here indicates that a different standard should apply to you with this animal. If the eggs may now be going bad, again I point out that there is nothing in the record that ties it to her injuries. Eggs going bad is all too common.
Despite her unusual rest position, she appears to have performed as expected in the breeding, gestation, and laying process.
Bottom line ? The body of knowledge and experience would indicate that you were fully capable of managing the conditions of her breeding and gestation as you would have been for any other chameleon. There is no basis for an ethical quandary here beyond considerations you were very capable of responsibly making, and in the end, it was your call to make. If anything, your work with her adds to the body of knowledge out there, and I would call the culling of the remaining eggs unethical on that basis alone. Again, just IMMHO.
Thanks for sharing.