The last of the published books has Jon Snow gang-stabbed by the Crows who are not aligned with him, and left for dead - without revealing his fate. If the series follows that line, we'll certainly see what Ser Alliser Thorne is made of.
On the one hand, he's busted Jon's balls from moment-one, and we know he's against bringing the Wildlings to Castle Black. On the other hand Ser Alliser knew that Janos Slynt was a coward, and deserved to be beheaded. Jon gave Ser Alliser a dignified command, and Slynt was beheaded because he refused to accept Jon's order for a less desirable command. So I think the jury's out. I don't remember from the books which side Alliser came down on.