The Skype wifi app is only to allow you to use Skype as a payment method at pay-for-service wifi hotspots.
The iPhone should automatically use wifi for data when it's connected to a wifi network. If you want to be 100% sure though, turn off cellular data when you're going to make a Skype call.
Unless I misunderstand the whole point of this question.
I think what is been asked is how can you limit skype without changing normal options to only allow skype app to operate only when on wifi. This will allow you to use skype as if computer to computer, not phone to computer and thus not use your phone data points for transaction. Notification can be sent of call received off wifi or some way you can tell so as to be able to return call once within wifi range, as this will be minimal data usage. I would also like to know if this is available and how to do it.
If this is not what the original question was meaning to ask I would still like to know how this would be done.
I don't think that's what the original poster was asking, but in any case, there's no way to do what you want to do. At least not automatically. You'd have to manually turn off cellular data each time you start Skype. Or at least just be sure that you are on a wifi connection before starting Skype.
It's an interesting idea though. Maybe it will be a feature added sometime in the future.