If he doesn't stay, then that means we can find out about the third side of the war.
But I also don't see Lavi, Lenalee, or the science department letting him go so easily.

But the church leaders may not want a Noah there.

That's true. Even if the others defended him, they'll either kick him out or try and kill him. Maybe.
But this depends if the Black Order survives this whole thing, because Lenalle and the other exorcists are having a showdown with the other noahs. It would be nice to know how they are doing. Where are the generals?
What's your guesses on what will happen. I don't have a clue @.@

To leave us guessing, they may switch to the other fights before showing Allen as a Noah

0.0
I have to say, I rather know what happens to Allen. Though I do miss them.

Exactly and by showing the others, people will continue to read wanting to know what happens to Allen

@tamtam YES! I WANT ALLEN TO BE A NOAH TOO~!

chiri-kun, haha, it's good to know that im not the only onewho wants him to be a noah
it will be exciting if he will join, right? 

Seems to me that the innocence is getting along with him, even though he's a noah. Besides, Allen's innocence resembles the 14th (it mentioned it earlier). If the innocence was going to destroy Allen if he went with the Earl, I don't think Katsura would have thrown the fact the Earl wants Allen to join with them in the first place. At least, that's my experience with reading manga.
So, my opinion, I don't think the innocence will think Allen is betraying it. Allen's innocence rate is over 100%, I think it would understand his views and the situation. I think? I'm confusing myself.
Lol, If I'm wrong, I give you permission to say, "I told you so loser!!"

No, Allen's sword is similar to the Earl's not the 14th's. I'm not sure if the innocence would let him join the Earl. The innocence has been shown to act on its own before.

yeah, like Suman's case...

Actually I meant Allen's innocence