Workaround: I have Greenify the BTSync app and it did the trick: after I trigger BTSync via Llama, the Greenify app kicks in when BTSync is done and puts it to hibernate.
Same problem here on CyanogenMod 10.2. I am using BTSync to periodically back up the whole SD card - which is great - but Llama can't seem to shutdown BTSync - i have tried simple event which basically unconditional root kill but, no luck.