How can you take her word over his?
Well generally, it often ends up being ones claim against the other (this is pretty obvious). It is probable that NBC had at least sufficient evidence to believe that the accusations were true. Things they most likely would have done would be to interview the claimant, the accused and any potential witnesses. If there were photos, text messages, or emails; that would help make the NBC's determination.
The key thing is weather or not the stories were consistent across the spectrum. Thus, if minor details about this situation matched the accused's statements, then NBC would be more inclined to believe the accused. The reality is that the more consistent and truthful a story is, the more likely it is likely to be a fact.
Will there be more accusations? Only time will tell, but in a time where sexual misconduct in the workplace seems to be mainstream, its highly likely.