That the scientist tried to kill him does not disprove the allegation that his wife thought Riker had sexually assaulted her. Troi stated that she did not find any doubt in her, that she felt assaulted. What did the episode leave out is that later events can lead people to start remembering things differently and they can convince themselves of things that never happened. Hence why eye witness accounts are actually the worst kind of evidence, even though they hold the highest rank in court.

So be fair it's not a well executed episode and the 90s were very different in the definition of consent compared to today. But even with that accounted for, it does leave the question if Riker is not pushing a bit too much, especially since his rank and standing can give him quite the leverage. There is a reason why most militaries will have a strict code of behaviour for every officer and the further up you go, the more strict it gets.

The only right way to end the episode would have been that Picard folds Riker verbally like a chair and makes it absolutely clear that he has to actively avoid getting in such situations. See code above. But then that would have been real live and not "Riker gets to smooch a hottie every episode" as the writers intended.