@jimbo: And I am saying that all the things you list off is the reason why Alliser is speaking up against Jon. None of them are reasons to kill him from Alliser's perspective the way he's built up. If they were, he would have done so before he let the wildlings through, not after.
He totally could have killed Jon earlier than he did. The very moment he should've killed him if he was going to, he decisively didn't, even though the other watchmen were looking at him to do it. It's just not a convincing character portrayal. The entire moment screamed: 'Ha! We shocked you didn't we?! You thought, if he was going to kill him, he would have done it here because that makes the most sense, so we made him not do it there and do it here instead because SHOCK!'.
It ends up just not making sense when the shock fades.
Was there really any shock though? I agree that I thought it was a weird direction for the Thorne character, but it was hardly surprising that he was a part of the mutiny, or that there was a mutiny to begin with.