I have heard it argued that Grant's success as a general was directly tied to his alcoholism, for much the same reason. He also knew what slaughter (of his own men as well as the enemy) would be necessary to conclude the war, but drank himself numb enough to go through with it.
I am not a historian, don't take this as truth.
> I think he was genuinely reluctant to ratchet up the slaughter of his countrymen, especially when he had the clear advantage.
Yes, they were his fellow countrymen in a sense, but they had declared themselves to be another country and were, in fact, his enemies. That reluctance is a serious flaw in a general.
>That reluctance is a serious flaw in a general.
Agreed. But regarding your other point, it was actually the official position of the federal government (Union) that the South was still a part of the union, and that the confederate government was illegitimate and in rebellion. So, still fellow countrymen. And I imagine he still admired Lee greatly, many did.
The slaughter McClellan was concerned about, and the source of his timidity, was that of his own men. That Grant & Meade had no such compunction is precisely why Lincoln turned to them. The Union victory then became a simple matter of attrition and its willingness to bleed.
I know he always gets this kind of criticism, but don't think he was an idiot, he knew his advantage. I think he was genuinely reluctant to ratchet up the slaughter of his countrymen, especially when he had the clear advantage.