It makes sense that Zachariah wouldn't have had all the angels in his pocket with wanting the duel to take place. Especially with the subterfuge that the party line was to put a stop to Lucifer. That's the official party line, and the most widely accepted righteous agenda.
So how would the majority of Heaven feel towards Cas? He didn't stand by the fink Zach, but he also didn't stand by the majority rule, and now he's sheriffing.
Did Raphael stand with the majority? Was/is he also an outlier like Zach and Cas?
Or maybe they purged the rebellion from her, and that was her sense of mission.
This actually makes the most sense to me. It was her own personal interpretation of Heaven's Will after reformation.
I don't think of Zach as an outlier. He was working for Michael, and that was where the power was. I think of Michael as having been in charge, Raphael as able to command the next level down, Lucifer fallen, and Gabriel abstaining.
So in Michael's absence, Raphael probably ascends to that position, except--spoiler factor of the oft-resurrected nerdy angel.
I meant outlier in the sense that, even though Zachariah and Michael and Raphael were the ones in power, that the general masses were kept in the dark as to their true agenda, that the general masses believed that the true agenda was to stop Lucifer immediately, not indulge in a M/L face-off of pissy bitchitude.
I would imagine the "Wait, we LET Lucifer escape? THAT was the plan all along?" revelation is what resulted in a lot of the angels deciding to throw in with Castiel or otherwise rebel against Raphael like Balthazar did.
Can you imagine poor Uriel's reaction. Oh man, I'm kind of glad for his sake that he is dead so he doesn't have to be so disillusioned.
Uriel wanted Dean dead (not Zachariah's plan) and Lucifer free.
So that's another faction, however many angels Uriel managed to "convert", that didn't care about the face-off, but thought that God was a shitty dad, humans suck, and wanted their brother Lucifer back. And he was the dude killing other angels, so whoever he converted would probably keep on trying to convert, killing other angels, and angling for Lucifer's jailbreak.
