I have a question for Clare. Why did Raphael bring him to the Institute in the first damn place? No, I don’t buy that Raphael was so scared of The Clave or of these kids that he brought Simon there. If it wasn’t for the distraction of Luke and his pack and then later convenience of the demon cycles being on the roof they would have been lunch meat. Anyone with just a little bit of common sense could have figured this out. And as for The Clave, I have already discussed in detail why The Clave are completely ineffectual as a law enforcement or a para-military unit. They have The Lightwood parents and kids patrolling a city as large New York City by themselves. Also, from what I have seen the vampires have been actively turning people. Simon is the latest example, but Raphael himself also an example of the Clave doing nothing about the vampire problem.
In 1953, when rumors of a vampire in their neighborhood became supported by strange disappearances of their children, Raphael and a group of older boys formed a vampire-hunting gang, intent on proving that they were no longer children and were capable of protecting their neighborhood from the vampire. They managed to track it down to its lair, the residence of several other local vampires, the Hotel Dumort. Guadalupe, who was, albeit worried, doubtful that the children would do anything rash, gave Raphael a gold cross to protect him from the monster she believes to be damned.
One evening, they raided the hotel in an attempt to catch and kill the vampire. At the age of fifteen, some time before he turned sixteen, Raphael was Turned by the vampire, named Louis Karnstein, who hoped that he would help him with his friends. However, the newly-Turned Raphael killed Louis, instead. In a frenzy upon being “reborn”, he then went on to feed on his remaining old friends, draining them of blood, which ultimately killed them.
— The Shadowhunter Wikia
I’m supposed to believe that The Clave has a long history of having a presence in every major city. It’s certainly what Clare has implied in her books. But if there was a Shadowhunter presence in New York City at the time, they sure didn’t make that apparent. From all I have seen, Raphael killed his maker, not The Clave. And the Clave didn’t visit any further justice on the vampire coven. For all appearances, nothing has changed with The Lightwoods moving to New York City.
So I ask again: Why did Raphael bring Simon here? Unlike in the show, Raphael has not shown that has any compassion at all. So that explanation is out the window. Actually, it would have made more sense for Raphael to kill Simon and make it look like an accident.