They probably would have hurt themselves more by keeping wikileaks and becoming the center of attention during the Christmas period, receiving the fury of conservative America, and losing major government contracts.
Amazon was screwed either way. This way however, they have compromised their cloud service's future (instead of their online retailer's present). It's not their fault they had to choose whom to piss off. They did however turn themselves from a whitebox solutions provider to a curated whitebox solutions provider though with this decision.
What do you think would happen if Amazon didn't shut down Wikileaks?