OK, so the gangers on the island only became independent because of the solar storm, so does that mean that they were the only ones that were 'human'? - so Amy's wasn't (because the original Amy's harness thing wasn't affected by a solar storm) and the discarded gangers weren't either - though they obviously had a consciousness of a sort, as they were suffering.
Or was the result of Cleaves report to the meeting a change in the process so that gangs were no longer capable of independence & independent life? In which case, Amy's ganger would have been produced by the new process & the Doctor knew that & so it was OK to destroy it?
Or - and I just thought of this as I was typing all that, the stuff he said to the ganger Doctor about it possibly not being the end meant that he knew that if a ganger was destroyed by the sonic screwdriver, it could be recreated later?
Also, did the ganger Doctor have a sonic screwdriver of his own (and if so, how did the Flesh create that?) or was it the original Doctor's? I have a vague memory of the original Doctor throwing it to him just before he used it to destroy ganger-Jen-monster - is that right? If so, did the original Doctor have a spare one in the TARDIS that he used to destroy Amy-ganger?
I think I have some intensive re-watching to do - lucky it's half term this week, so I'm not at work...