The term "morally ambiguous" can be interpreted in several different ways; it is not necessarily a negative trait, but is often interpreted to only include the negative. In this case, it should be used to accentuate a character whose morals are fluid, or who holds opposing opinions on different subjects; a morally ambiguous person is not good or evil, but complex both beliefs and actions.
In March, most of the characters are morally ambiguous in one way or another. Even John March himself is not exempt; he starts the book as an idealist and ends it with doubts about himself and his role in the world. However, the most morally ambiguous character in the book might be Augustus Clement, the smooth-talking plantation master. Clement seems to be a very honest and fair master to his slaves, but March discovers that Clement is not treating them well because of their innate humanity ("all men are created equal") but rather because he believes them to be an inferior race of humans who need to be owned for their own good.
"They, too, are children, morally speaking, and it is for us to guide and guard them until their race matures. And I believe it will, Mr. March. Oh yes. I am not one of Morton's skull-spanning acolytes. I do not think the current order immutable."
(Brooks, March, Google Books)
This condescending attitude shows that for all his enlightenment, Clement is simply another racist at heart; all he can see is the status quo, although he claims the contrary. He never truly believes that slaves will "mature as a race," but is content to continue the current ways. Unlike the cruel Ethan Canning, who treats his slaves harshly but eventually saves March's life, Clement retains his prejudice.