The thing I don’t understand is, why the baby/pregnancy? To give Mary a motive for going after CAM, maybe, but isn’t putting John in a bonfire enough? And her pregnancy immediately makes her vulnerable, so they can ignore her background and make her a victim. But then why go through the trouble of making us feel conflicted about her with a half-baked redemption if we’re supposed to ultimately sympathize with her? Do you have any speculations about the purpose of the baby/pregnancy?

I have many speculations, but they don’t really boil down in a useful fashion.

Maybe Mary being pregnant is the tipping factor that leads John to take her back.  Maybe it’s what leads Mary to a decision other than just blowing CAM’s head off and being done with it (and thus ending the threat before Sherlock can).  Maybe it’s just like you say, and they wanted it to make her more vulnerable so we would sympathize with her more (though this is such a stereotypical move, it always backfires and pisses me off :P).  

Maybe it was to create more of a sense of threat to Sherlock and John’s relationship.  Mary in herself isn’t enough to make John stop going around to Sherlock’s, but the baby could be…

Maybe Mary being pregnant is a plot point for next season.  Maybe it becomes a point of leverage, or vulnerability for her.  Or maybe John turns out not to be the father.

Too many possibilities at this point, and nothing that really points at one being any more likely than another.