I think they wouldn't have cracked down on it so much if there wasn't in-app purchase crackers (IAPCracker, IAPFree) that directly threatened their revenue bottom-line, and forced developers to deal with in-app piracy.

I think, if a deal was struck with Saurik/Cydia Team and Apple to explicitly not do that, there was a much better chance the jailbreaking community would have held.