It does get complicated, because even the shadow of Lasciel knew Michael, knew how Harry felt about his friend. She never expressed any thoughts to Harry that Michael was a threat. Perhaps that was part of a clever plan of the cunning Lasciel that backfired, or the Shadow didn't even try because she knew that on that point there was no convincing Harry. The Shadow was changed and became Lash out of love for Harry, Lash was redeemed. The Knights are all about redemption, even for the Fallen.
But back to Bonnie, yes, as of now she is an innocent, a child, but she still has the memories of Lasciel doesn't she? Her memories must extend before the angel rebellion that caused them to be expelled from Heaven. Remember the brief scene in St Marys when Lash wistfully mentions the beauty of the church and how she misses that? Or when she helped Harry to play the guitar, making music was another thing she couldn't do after the Fall.. Perhaps because she is half human spirit, and because of the changes in the Shadow when she became Lash, Bonnie will also have a choice? At the moment she doesn't see the Knights as enemies, but at some point she will have to pick a side.