I think the deciding factor for Don really was Megan's assured, relaxed way with the kids. Faye, you recall, couldn't really deal with the kids, as well as knowing his secret.
It was interesting how, at the end, Betty really didn't like hearing that he was getting married. Emotionally right, but more than a little unfair, in that she got married the minute the divorce went through (in fact, meeting Francis was the main reason she was so eager to get divorced.) But perhaps she doesn't want Don to settle down and find some happiness. Besides, when he was still running around with bimbos it allowed Betty to talk trash about him. With Don respectably married she might have to shut up. Although one does wonder how long it will be before Don starts cheating on Megan.