Fair enough, but that doesn't change anything. The Doctor is fine with gassing them, but freaks out about shooting them. It's hypocritical.
What???? It was explicitly stated that it was about ending their lives humanely rather than cruelly. There was no way they could be allowed to live -- indeed, their own gigantism was making them suffer as well as posing a threat to humanity -- but it was a choice between giving them a peaceful end and inflicting a violent one.