Whether the discarded flesh retains some echoes of the memory of the human that used and discarded it or not, isn't really relevant, imho. The bottom line is that the Flesh has sentience *separate* from it's human user, an awareness that is shoved aside, when humans forcibly take control of it. That awareness still exists, when the humans are done and toss it away.

The whole point of the two-parter is that the Flesh are people, not equipment to be used and discarded. Yes, Jennifer!Ganger retained more memories, than the others, but the point is, she remembered. The memories and potential are there.

Not if the flesh while it is in the form of Amy shares her consciousness- which it does.

What does sharing Amy's consciousness have to do with it? It's not sharing her consciousness after the Doctor cuts the link. That's the important point. What happens to the Flesh's original consciousness, that was shoved aside by Amy's mind by their link? It appears as if it is destroyed and that makes the Doctor's action murder.

At that point its one entity distributed over two bodies, but only aware of being one of them

No. There are always two bodies and two entities. There's the Flesh body and mind and Amy's body and mind. Amy's mind temporarily takes up possession of the Flesh's body, making it appear to be her and suppressing the mind of the Flesh, who is somewhat aware, but lacking in autonomy. Amy has control, but she is not the only entity occupying the body.

Well, nothing was resolved by the next episode, to my disappointment. In order to maintain my respect for the Doctor and handwave Moffat's mistakes, I'm going to assume the TARDIS or the Doctor had made plans for the Flesh and that is is somehow alive and being cared for.

Moffat really needs to be more careful with these morality issues. I'm having to handwave a lot this season. *sighs*