I took something a little more philosophical from it. It had a whole theme around the 'origin', and that what you were in the past you are now (EG Lio and the predators, CREEPY!) and that once you lose your ignorance about reality, there's no getting it back -- like lost innocence. Also, the whole deal with 'you can only kill one person in your lifetime'. It seemed to me it meant the only one you could kill was yourself -- either through suicide or losing your humanity by murdering someone else, and again, kind of a loss of innocence kind of deal. If you kill yourself, you'll only recover that tragedy in a future life if you discover your 'origin', and if you murder someone you lose what makes you a person. I believe Touko once said something about how we don't sin, but that we carry the sins of the path we chose...
Also, it kind of tried to push that everything was inevitable -- who you are, decided at birth, puts you on a track that you can't get off of, because the choices you make were pre-determined by who you are. Tomoe was a great manifestation of that. Araya was all like, "you are a fake, your feelings for Ryougi were programmed into you so you would make the choices you made". And he did make those choices, because he followed who he was and how he felt -- like a doll (XD Touko reference!) It is a bit ironic that the person guiding the main characters, Touko, was a doll-maker. I think that was intentional.
Damn, no wonder the title means Garden of Sinners. XD