When Joshua is about to transform the enemy soldiers yell, "Kill him quickly!" I think they wanted him dead, but the Queen wanted him alive to enforce her new found power. I'm guessing her deal was Joshua would be spared, but they altered it. Of course we all know the connotations of the Phoenix and the possible twist involving that.
All speculation. Since the game is in the wild people probably already know the specifics. Hopefully nobody will spoil the game.
Another thing I'm curious about is the guy in the cloak making Clive trip out, and I assuming causing him to transform into Ifrit. Also the man on fire. I'm looking forward to seeing if those were real or a hallucination. Initially I thought the cloaked guy turned into Ifrit since Clive was yelling, "You murderers!" On the second time through it seems like he was possessed by the man on fire, the spirit of Ifrit.