The dynamic between them, and therefore how they do business with each other, is going to be different. This isnt a perfect example, but its sort of like.....okay, you live with your parents as a kid. Then you grow up and move out. If your parents end up moving into your house with you years later, once again you're living with your parents, but its a totally different thing. You're an adult, its your bills, your family, its your house.
As for Eve being knocked up....everyone keeps saying that we've seen this before, but really, we havent. The first time, Eve found out, we had a few issues where she was all awkward and not telling Mark, and then he went into space. By the time he got back, it was all over and we barely saw any real fallout from the abortion at all, what with all the other drama going on it was just one more thing on the sh*t pile.
This time, Mark knows early on. How they decide to handle things will be a decision they both get to make. How it impacts their relationship is something we will get to see.
I think maybe this is Kirkman's way of playing around with the genre concept of the "ever returning status quo" where after all the empty shock value things go back to normal. Sure, aspects of this feel pretty familiar, but I bet you just about anything its not going to play out like it did last time.