Ok, to explain:
Amy was in a harness, but it was different tech to the gangers they dealt with at the mine. It was more advanced. The Doctor wanted to wake Amy up and, presumably, have a fighting chance wherever she was.
It wasn't a seperate, conscious flesh like the gangers were. It was of the sort that deactivates when you seperate the connection.
The Doctor didn't destroy the flesh, he severed the connection. The flesh was destroyed as a result.
One continuity error - he gives a screwdriver to his ganger, but then pulls out a second one in the control room?
Or did I miss something?
Also, in response to the question about Jen transforming - the surviving gangers were accepting their humanity while Jen rejected it, hence the 'monsterification'. A fairly obvious card as there were more subtle ways they could have done it, but throughout the last two episodes when they were human they became 'stabilised' but when they were acting as gangers they looked less human.
Edit: Also, I can't help but think they're going to do something about the Doctor's "humanity" along the lines somewhere.
Also, River Song hinted that she killed the doctor, but we all know spacesuit girl killed the doctor.
Spacesuit girl is Rory and Amy's kid.
Therefore: Spacesuit girl is River Song, unless River killed another 'greatest man who ever lived'.