Ubisoft has stated more than once that Assassin's Creed 3 and its PS Vita spin-off, Assassin's Creed 3: Liberation won't shy away from potentially sensitive issues like slavery. After all, taking some creative license with historical accuracy is one thing, but it would be extremely disingenuous to try to portray the American Revolution without involving any slaves.
Fortunately, Ubisoft has managed to treat the issue (and, presumably, others) with respect by ensuring that Connor will always take the moral high ground. In conversations, he admonishes others for pontificating on morals while owning slaves, and of course he himself owns none on his considerable estate.
Of course, we're not really sure how a half Native American became so wealthy during this time period, but we're anticipating that that will be explained at some point in the full game. Now we're just aching to catch a glimpse of the licentious (and supposedly accurate) version of Ben Franklin that Ubisoft's been going on about.