Answer
Yes, in that sense they wounded his body.
If everything had been followed exactly as Srila Prabhupada instructed, there would have been no harm. When we say ISKCON is his body, we do not mean a physical body. Rather, we mean that his mission, institution, organization, and preaching work are extensions of himself.
His institution is extremely dear to him.
Therefore, when deviations occur, they can be compared to wounds inflicted upon that body.
Just as a physical body can tolerate wounds up to a certain point, an institution may also tolerate damage for some time. If the damage becomes severe, the soul may eventually leave the body.
How much Srila Prabhupada has chosen to tolerate is known only to him.
However, over the years there have been signs of improvement. Not necessarily because of deliberate reform, but because painful experiences forced people to reconsider certain assumptions. Repeated difficulties and failures exposed weaknesses in the original post-1977 understanding.
From the perspective of the parampara, the situation became spiritually embarrassing because the exalted position of guru appeared diminished through repeated failures and controversies.
This happened not because Srila Prabhupada failed to provide instructions, but because those instructions were not followed.
The July 9th letter clearly explains how first and second initiations were to be conducted within the institution. It is difficult to imagine a more specific institutional instruction than that.