Neku is talking to Joshua. He says "You took care of things right, because otherwise Shibuya would be gone". That alone suggests that it wasn't Neku who stopped Shibuya from being destroyed. Joshua didn't destroy Shibuya because Neku made the right choice.
Plus Joshua is pretty clearly still an angel in the bonus ending.
I don't think it's implied at all. As far as I see it, it says the exact opposite.
Spoiler
Damn, he's no Angel. He's the god of Shibuya.
But seriously, it's typical like Square Enix, or in general, the devs and writers to have confusing endings that make us really think.