This is kind of hard to answer for a couple of reasons. First, do you have a source for this quote? I've never read it before, but if we do have evidence that Lincoln said it, the context would be very important. For example, WHEN Lincoln said this, and to whom, would offer a lot of insight about what he meant and whether this was "true."

And regarding that, I'd follow up with a second question: mainly, what is it that you are looking to establish? Whether Lincoln thought southerners in rebellion were justified in their actions (based on everything we know about Lincoln's views on secession, this could never be so)? Are you asking, to modern observers, if the actions of the seceding states in 1860-61 are understandable? Well...not really. Slavery and treason haven't aged well. If you're asking whether people in the north were all that much different than people in the south, then I think you're getting into muddy waters. You could argue that many of them were very similar, but also very different (stupid answer, I know...but it's too complicated to answer with a straightforward yes or no). Some people in the south never owned a slave and thought the institution was wrong and/or wicked. They nonetheless probably harbored racist sentiments, much like their northern counterparts. In this way, these people were indeed very alike. Yet they often came from different cultures within American society (urban vs. agrarian, mine workers vs. farmers vs fishermen, etc). Their economies were often very different, and depending on the specific city (say, Boston vs. Charleston) social values varied wildly.

If Lincoln did indeed say the quote you mentioned, I think the much more interesting discussion is about what Lincoln meant by this vis a vis an exploration of his audience and the period the speech/conversation took place. I think that the short answer to your question is a very fuzzy (and probably unsatisfactory) "well, yes AND no." If you want a little more insight into Lincoln's political maneuvering, and how he carefully crafted policy via his speeches, a great place to start might be Doris Kearns Goodwin's 'Team of Rivals.'