On the surface, they're contradictory. But with a little creative wiggling, I think you can adjust Ro's appearance in the comic to more or less fit with the DS9 Relaunch. I think it's a bit easier than fitting in the pre-relaunch novel Wrath of the Prophets
Don't worry about contradictions, all things considered, they're few and far between, and the majority of the stories in Malibu's run are good. Far better than Marvel's attempt at a DS9 comic a few years later. There's a Tom Riker story of which I'm particularly fond.