As a person who has made the conscious decision not to have children, I (personally) have had friendships drift apart when almost everyone else around me starts having babies.
This is just my experience, but when friends start to procreate, they are (understandably) not around as much. Their interests change to incorporate this new creature. And often times, they become more boring to be around (party discussions that used to be about philosophy, science, politics, technology, etc instead become about diapers, day-care, and crappy kid shows). This is as seen from my perspective - I can understand fellow parents bonding over similar circumstances. My point is that oftentimes, life paths of friends begin to diverge when one starts having a family and the other does not.
I cannot help projecting my own life experiences onto my interpretation of "Sherlock".
Therefore, I see that the "safest" route for Mary and baby story-wise - that they simply melt into the background - is highly unlikely. Having children changes ones desires and perspectives, which would lead to a chasm between childless friends. As a father, John might be less willing to risk his life. He might fall in with other people who share his experiences, now having more in common with other couples with kids than with Sherlock.
Even simply getting married caused a distance between John and Sherlock. Granted, it was his honeymoon time, but just being in a marriage caused John to neglect his friendship with Sherlock for over a month (and it was only through coincidence that they even met up again that soon). Having a baby would only be worse. Even if John wanted to resume crime-fighting at some point, he would still need to spend a lot of time with his wife and child at first - then, over time, he might soften to the family life and gradually lose this desire.
If this show is really all about Sherlock and John's friendship, then I honestly do not see a "happy family life" going on in the background. Instead, something must happen that severs him from this role. Whether it's death, betrayal, or separation (e.g. Mary and baby going into hiding), I really feel that John is going to have to take some serious emotional hits so that the story can keep him close with Sherlock. And Mary and baby are, unfortunately, the people who this must happen to.