No, the reason why the witch's cult came after Emilia is because she is a half elf, among other things. But being a half-elf would in general garner much more interest from the cult, compared to being just an elf.
Felix literally regenerated a bunch of his flesh after the explosion btw, being the strongest water magic user, i.e. healer is no joke.
Those barrier stones only work against mob beasts, they wouldn't do much against cultists, if anything really.
A lot of your questions regarding Puck and Emilia's relationship are answered in the prequel movie, the frozen bond, however you'll also end up having a few new questions after that too.