There are a lot of games that use Cocoas2D in the App Store, that also includes a physics engine. Box2D should be fine.
I have two games on the app store using cocos2d, and there are a heap of other apps out there using box2D. While my apps have been rejected for other reasons, use of a 3rd party library has never been one of them.
The Rolando games use box2D, so I think it's safe to say Apple won't reject an app for that reason.
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