I think that, while both may work, I would use the second option here. "Was marked by" has, to me, negative connotations - as if the abolition of slavery was some sort of a stain, a big negative thing that defined the century (a mark), which I, and most people (I hope) very much disagree with. The second option also seems more natural to me. If you wanted to talk about something negative you may choose to use the first option, but to me it really does just imply a large negative defining event. Perhaps that's just me though. Since both are grammatically correct it's ultimately up to you which you choose, I just thought I'd offer up my opinion.

I think that, while both may work, I would use the second option here. "Was marked by" has, to me, negative connotations - as if the abolition of slavery was some sort of a stain, a big negative thing that defined the century (a mark), which I, and most people (I hope) very much disagree with. The second option also seems more natural to me. If you wanted to talk about something negative you may choose to use the first option, but to me it really does just imply a large negative defining event. Perhaps that's just me though. Since both are grammatically correct it's ultimately up to you which you choose, I just thought I'd offer up my opinion. In a more academic context you might want to use option 1 purely because it is "more" correct - see j D3V's answer. But in general use both work.