Maybe it's because I haven't read all the stories yet, but so far I don't understand where the "canon" that Holmes is a cold, heartless machine comes from. I just haven't seen it in the stories I've read so far. Logical, rational, focused; yes. But those are not synonyms for cold and heartless. I don't get it....
Yes, Watson does point out that Sherlock is 'inhuman' and a 'machine' more than once in canon.
One of the first examples in The Sign of Four p.22:
"What a very attractive woman!" I exclaimed, turning to my companion.
He had lit his pipe again, and was leaningback with drooping eyelids. “Is she?” he said, languidly. “I did not observe.”
“You really are an automaton,—a calculating-machine!” I cried. “There is something positively inhuman in you at times."
I also think that Sherlock's act of murder should not be taken so gravely by fans. I was worried about it up until the point where Mycroft lightheartedly asked Sherlock if he enjoyed the 4 minutes of exile and asked him to return. This means that the old Sherlock is back - the enemy has been dealt with - and I doubt similar methods will be employed with Moriarty.