I was just thinking to myself a few days ago, while I was finishing City of Heavenly Fire; that none of the stuff that happens in the books would have happened if Valentine's father wasn't killed by werewolves. That's when Valentine started to go crazy and change the values of the Circle; to get rid of Downworlders. It all started with that. If that didn't happen, the Circle could have been an elite group of Shadowhunters and not a stain on Shadowhunter history. He wouldn't have given Jocelyn demon blood and Jonathan wouldn't have turned out the way he did. And he would still be alive and they probably would have been a happy family, but I don't think Clary would have been born though, and either would have Jace, because Valentine wouldn't have forced Stephen to split up with Amatis because of Luke been a werewolf and marry Céline and Stephen and Céline would still be alive. Amatis wouldn't have been targeted and turned Endarkened and would still be alive. The Lightwoods wouldn't have to try so hard to protect their family's name because of their involvement with the Circle, they would be proud of it and Max wouldn't be dead. But I don't think that Alec and Magnus would have gotten together, but one can hope. But then again, Simon wouldn't have known Clary and therefore not have known about the Shadow World and become a vampire, lost his memories and then to regain them by becoming a Shadowhunter, not that that's a bad thing
Maybe I am just thinking to much about it but that's what I think could have happened if Valentine's father didn't die.