I think some magic must be involved. From what we've seen of the witches that work with vampires they seem to have a rather grey morality, helping vampires that kill etc. Bonnie seems to have a much more strict sense of right and wrong so if she was involved in the "ripper" Stefan story it would be fascinating to see her in that role.
That relationship between witches and vampires is strange and I don't really have my mind wrapped around it. Hopefully they'll go more in-depth on the show.
It would be cool to give Bonnie her own storyline with Stefan