When you have a dog that has been through what she has (not to mention being all hormonal), there is a certain degree of understanding body language and behavior that needs happen.
I would begin, perhaps under the guidance of a trainer, by instructing your boyfriend to simply not look at her, talk to her, or acknowledge her in any way. She is uncomfortable about your boyfriend for some reason. It could be his disability, it could be the fact that she’s possibly been mistreated by men, or that she’s afraid of a male presence for the safety of her pups. She needs to understand that they can both be in the same room and he’s not going to harm her.
Once they are both ok with this, have him begin to offer her treats, again with no talking or acknowledging of any kind. Just have him drop a treat every now and then. Work it up to him giving her the treats dirrectly, and then to him gently petting her while she takes the treat. Do not allow him to lean over her, or touch her face. If he is to approach her, have him approch her from the side, and always, no matter what, make slow and deliberate moves around her until she understands that no one is going to hurt her.
She’s afraid of him for some reason, and the goal is to desensitize her and teach her that he is not going to harm her. I would also suggest that if you, or someone you trust to properly handle the dog, are not around to take charge of a potentially dangerous situation, that she be crated or kept in a seperate room from him. If you are not comfortably with her being around him while she pregant, I would recommend having someone foster her until her pups are born and weened, and she is spayed. Hormonal and fearful dogs are more likely to act on instinct rather than training and conditioning. And being fearful or nervous yourself around such a dog does not help the situation. You guys are doing a good thing by taking her in, but don’t get in over your head and make matters worse by not properly dealing with aggressive and fearful behaviors.
