How to force rules configuration to load
Your question is a bit confusing, because the default Rule in question is defined by the Payment module in commerce_payment.rules_defaults.inc, not by the PayPal module. It sounds to me like a general case of cache trouble, though in my testing and development of the PayPal module I've never seen any issues with it. If what you mean is simply that the payment method rule is disabled by default, that's just how we've built the modules - enabling it like you show with your custom code will just be a necessary step.