Good post, i have no doubt that next season we will have another Ben-centric ep which will cover this topic. If he got her pregnant and died, that most likely only solidified his hatred for the Dharma Intitiative. His father (Uncle Rico) asked if had a date when Ben kept looking at his watch and Ben had a wry smile after that.
If Annie was still there, then I feel bad for everyone, because Ben is pure evil.