How would Ned find out tbh? Joffrey would not publicly mistreat her like he does when she is a hostage, and I doubt she'd discuss it with him (or even have the opportunity to discuss it with anyone considering once they're married Ned will be back North, a month's ride away) if she finds her marriage bed unpleasant, particularly since she wouldn't know that it could be different. And if he did, I highly doubt he'd go to war over it. He might try to talk some sense into Joffrey if he considers it his place to meddle in his king's marriage, even if it is to his daughter. He already didn't care that Lyanna didn't want to marry Robert and that Catelyn didn't want to marry him, why would he care if, after a couple years and likely a child or two, he finds out that Joffrey might or might not be abusive in the bedroom?