Who’s to say what the legalities of marriage and divorce were defined as in FTL.
In the real world, I don’t condone adultery at all, so I do have issues with Milah having run off with Killian. But looking at it from his perspective, he loved Milah, and he’d probably heard an awful lot about Bae. So actually meeting him, something he never thought would happen, would have been an emotional experience for him. This kid was part of the woman Killian had loved, so it’s understandable that he’d have wished for some connection with him, especially considering that Milah was gone.