It’s funny, I worry about lots of stuff about the movie (mostly of the “how will it turn out?” and “Will they cancel it at the last minute?” variety) but I don’t worry about that.

It’s just not that unusual a story element. Actual incest comes up all the time in mythology and folklore (super-famously, King Arthur slept with his half sister.) In Empire Strikes Back Luke and Leia, who are actually brother and sister, share a long, passionate kiss (that CONFUZZLED ME GREATLY when they turned out to be related in Return of the Jedi.)

But it’s not like there was a big fuss when Jedi came out. Veronica Mars runs a plotline where she thinks she dated her brother, but then it turns out they’re not related; no one seemed all that bothered. I could probably think of a bunch of others like that. People are pretty used to it as a plot element. It’s just not that mindboggling. I suppose if Jace and Clary were actually related that’d be one thing, but they’re not, and I imagine most people will either assume that or assume they won’t wind up together (a la Luke and Leia.)