Since your cat was a stray, it's possible that she has had a bad experience with men, which, being a cat, she's transfered to all men. It can easily be overcome with time and patience, and it sound to me that the pair of you have both!!!
First, it's important to understand that it's not personal, it's instinctual... once fightened or hurt by a man, she is naturally catious. The growling doesn't mean dislike... it means fear. And that can be alleviated.
Second. it's significant that it happens when your SO picks her up... for a feral cat, this can be a most distressing situation, since all of her instincts rebel against giving up control of her physical self... in the wild, the ability to fight or flee requires control of movement, which she gives up when someone picks her up. So, right now, suggest that your SO refrain from picking her up for awhile. Instead, concentrate on petting her by kneeling (ie/getting down to her level). Progress to gentle handling of her body... Let her get used to him handling her before moving on to picking her up. Suggest that he uses a "warm" speaking voice, talking to her gently while he pets her. If she shows impatience, he should back off... this reinforces that she is in control and can set her boundaries... which in turn makes her more confident with him. After a few weeks, start picking her up again, always setting her down and reassuring her if she growls. Over time, she'll be more accepting of him.
Third, how you pick up the cat can have an influence. It's very normal for us to turn a cat over on her back like a baby... for a feral cat, this can be a real trust issue. Exposing her belly means submission to other cats and it also exposes her most vulnerable place (her belly). For a cat who's been feral or stray, this can be very distressing, so should be avoided until strong trust has been bulit up.
It's best to pick up the cat so that she's upright, using as little "force" to restrain her as possible. If she wants to get down, she should... it's important not to make it a power struggle. On the other hand, it's important to be persistant: your SO may have to handle her in a crisis, and as a result, she needs to build a bond with him that is strong enough to handle stressful situations.
Thanks again for rescuing this little cat and giving her a caring home!