Lyric discussion by IllToast2That 

Cover art for Hay Loft lyrics by Mother Mother

I don't believe there's anything about molestation in this song. I think it's a song filled with metaphors. Daddy and his gun could represent anyone in an authority position (or someone just plain controlling). And that person is gunning for someone who is involved in a romantic relationship...perhaps that which "daddy" doesn't improve of...(dang preposition!)