I'll look at 'Gone to the Farm'
Valentine would obviously still be interested in the cup, and not realizing that it was in Dorothea's possession, would likely expect Jocelyn to keep something so important with her. So, in my opinion, a likely scenario is that of Valentine tracing them there and then sending his demons in. Clary however, would be in 'extreme angst mode' at this point, having been taken away from Simon, and the newly met Jace. So likely, after this attack, her response would be much more extreme and potentially harmful, not having Jace and the Clave immediatly around to explain the shock. She might blunder along for awhile. Eventually, Clave would probably get wind of this and send somebody out, with them probably having to chase after a suspcious and freaked-out Clary. She may even end up at a different institute, depending on if there's one closer to the farm. So she might meet Jace, or she could meet other Shadowhunters who wouldn't be so tolerant of her 'Mundieness' after getting all the demon details from her.
I think that different Institutes would have sort of different brands of Covenant, some might not be as principled as the New York stuff, some may be more aristocratic in organization, others could purposely oppress (but not outright harm) Downworlders, and some might be totally Old-school. I just kind of see it as a different way of viewing the Clave, and seeing how some might be more sympathetic to Valentine.
That was surprisingly interesting to write. I never got into that aspect of HP.