I am not asking if this is okay:
Object.prototype.method = function(){};
This is deemed evil by pretty much everyone, cons
I think it's fine if it works in your target environment.
Also I think prototype extension paranoia is overblown. As long as you use hasOwnProperty() like a good developer that it's all fine. Worst case, you overload that property elsewhere and lose the method. But that's your own fault if you do that.