My thoughts are that unless the players are willfully engaging in dangerous shenanigans (i.e. "it's how I roleplay" or they are not roleplaying at all and thus attempting things their character never would) then ultimately the failing is on you as a GM. Your example with the assassin is pretty revealing in what areas you need to change. RPGs are about story, but they aren't a story in the traditional sense of a film or a novel and as such you need to take play balance into consideration when you are drafting challenges for your players. The assassin was essentially an unbeatable opponent and you built him that way as much story might be behind it it's essentially "rocks fall, everyone dies"/Killer Game Master (http://tvtropes.org/pmwiki/pmwiki.php/Main/KillerGameMaster). As GM you hold all the cards, and you need to wear two hats: One where you are the narrator for the world and the game master creating dungeons and scenarios that are fair and level appropriate for the players, and the other where you are the antagonist playing the villains and monsters you have created against the player. Those two roles should be fairly compartmentalized because the second you mix them then the world design itself is overtly antagonistic and the villains and challenges posses a kind of meta-knowledge/genre savvy that allows them to easily overwhelm players.

My thoughts are that unless the players are willfully engaging in dangerous shenanigans (i.e. "it's how I roleplay" or they are not roleplaying at all and thus attempting things their character never would) then ultimately the failing is on you as a GM. 

Your example with the assassin is pretty revealing in what areas you need to change. RPGs are about story, but they aren't a story in the traditional sense of a film or a novel and as such you need to take play balance into consideration when you are drafting challenges for your players. The assassin was essentially an unbeatable opponent and you built him that way. As much story might be behind the assassin's deadliness, it's essentially "rocks fall, everyone dies"/Killer Game Master. 

As GM you hold all the cards, and you need to wear two hats: One where you are the narrator for the world and the game master creating dungeons and scenarios that are fair and level appropriate for the players, and the other where you are the antagonist playing the villains and monsters you have created against the players. Those two roles should be fairly compartmentalized, because the second you mix them the world design itself becomes overtly antagonistic and the villains and challenges posses a kind of meta-knowledge/genre savvy that allows them to easily overwhelm players.