First, it sucks that the girl feels the need to seek shelter from her own family. Even if her family doesn't actually want to kill her for her conversion, the mere fact that 'honor' killings are common enough that it is plausible, even likely, that it may be true is a tragedy.
Second, it's possible that her new church planted the seeds of her fears. Anytime I see the word 'megachurch', I cannot help but assume the worst. Megachurches seem to be the incubation point for much of the worst in American Christianity, the ignorance, bigotry and outright lies that get preached as truth.
Finally, I hope that all of this will cause the girl to think more deeply into her decisions. Trading one evidence-less belief for another does not seem to be much progress to me, particularly if her new church is one of the more fundamental ones.