This is not completely true. Even back then, certain computers running skype could become "super nodes" that handled incoming connections to devices e.g. behind NAT. All you needed to do to wiretap was become one of these nodes, which wasn't hard to do.

But yes, if you made sure neither computer had NAT and used no super nodes it was possible to be pretty protected (except for the problem that PRISM is tied to the network hardware and can read anything anywhere on the internet).