So why would Juno kill Lucy and say "the cross(templar logo) darkens the horizon?"
Your theory has so many flaws.
1. It would be a triple twist so that would get a bit ridiculous.
2. Juno's actions and words wouldn't make any sense.
3. Clay's words wouldn't make any sense, "she's not who you think she is".
And IF he was talking about Juno and not about Lucy he would have told him that in the black room.