Bea left Bill because she was afraid that BB would be brought up in a life surrounded by chaos and murder if she had stayed. She wanted better for her daughter. Bea loved Bill, no question. She even explained this to him at his house (dialogue right after the Karen Kim sequence). She left thinking it was the right thing to do for her unborn child, not because she didn’t love Bill. She didn’t want Bill to know about BB because he didn’t want him to claim her, so she had no choice but to disappear, run away from him. She wanted BB to have a “normal” childhood, with a nice “normal” father, that’s why she was going to marry Tommy. Even at that time she was still in love with Bill, not Tommy (look at the way Bea interacts with Bill during the chapel scene if you don’t believe me), but it wasn’t about her anymore, all she cared about was her unborn daughter. When Bea and Bill have their discussion at the chapel Bea still feels the same way, so she couldn’t let Bill know that the baby was his. She still wanted her daughter to grow up with Tommy as her dad, not Bill. The only reason she tells Bill the baby is his at all is because she is desperate to save her baby’s life, not her own, when Bill has the gun to her head right before he shoots her. As far as the reason that Bill never married Bea is anyone’s guess. Tarantino didn’t give up much info about Bill and Bea’s relationship, but one can certainly imply that it was unusual. The deadliest woman in the world and the deadliest man in the world, doesn’t sound like a match made in heaven, but rather a match made in hell. Bill doesn’t seem like the marrying kind and right before she got pregnant, they seemed to be happy with the way their relationship was, not needing to get married. Do you really think that Bea should have expected to get pregnant? Were they doing a lot of screwing around? Did they use some kind of faulty protection? Who knows what happened, all we know is that it did!
Whew, that was a lot, but I wanted to give you my thoughts ;D