Who do you think broke off the engagement? Molly realizing that she was just using Tom as a substitute for Sherlock, or Tom maybe realizing the same thing?

Doesn't help her get married and have kids...

If I had to decide, my bet would also be on Molly breaking it off. She has been very in control this series, showing much more confidence and an understanding of what she deserves and what she does not have to tolerate. Her description of their relationship in TEH seemed very happy and comfortable, but at no point do we see them really connect, or that there is any passion in their relationship. My thought is they would have had a stable marriage, but it would be more as good friends/partners, rather than something based on true connection. Sort of like a stereotypical couple from 60/70 years ago where the man was expected to be a protector/provider, and the stated purpose of marriage was less focused on the fulfillment of the individual than the creation of a family unit. Not in itself a bad thing, but somewhat outdated to many in our modern world. In the post-lib world that Molly (and myself) were raised in, marriage and relationships are meant to be fulfilling for the individuals involved, not just because they are expected. Molly knew she could build a good life with Tom, which is likely why she agreed to his proposal in the first place, but overtime decided it wouldn't in itself make her happy (impetus for that realization major topic of debate in this thread), and thus broke it off. 

The time between TSOS and HLV is unclear, but given the most likely timeline, it wouldn't surprise me if events at the wedding were the beginning of the end.