to imbue his work with a semblance of humanity, even at times when we're not supposed to like the character at all.
Absolutely. Which is the thing which IMO he excels at, which drew me to Lee in BSG - even when he's pissy in the miniseries and when he makes selfish decisions or lets his idealism get the better of him though he should damn well know better. It's not just that he's pretty. I don't expend this much flail on someone just because they're pretty. *g* You gotta BRING IT.
BTW, the way you phrased that ties in pretty well to what Jamie says in the interview about the reason he wanted to do John Doe, too. ;)