Sorry but yes, if he committed a crime, he should be charged. There's nothing nuanced about the law.
If the woman reported the sexual assault and felt as though he had sexually assaulted her, whether you deem it a sexual assault or not is irrelevant. If she wanted him to wear a condom and he refused and had sex with her anyway, and Swedish law allows for a conviction in this regard, it's really simple. If someone you like murdered someone you dislike, they shouldn't be exempt from charges of murder just because you like them.