The way to do reverse engineering legally is to have one team reverse engineer the target and completely document how it works. Once it's documented, another disconnected team writes a new implementation from the documentation.
So you'd Skype's co-operation to do this? They are able to prevent reverse engineering by not writing the documents?
Suppose you and I work for the same company. I bust open Skype through decompilation, reading memory, the network, whatever trick I want. With that, I write documentation for how Skype's protocols work.
You read my documentation, and implement it in a new program. Since we haven't talked, and you've never seen a line of Skype's code, you haven't infringed on any copyrights.
It is important to note, though, that this does not necessarily protect us against a patent suit.
If it is done correctly, co-operation from skype is not required. The team that does the reverse engineering will write the specs and documentation from what they learn by examining and analyzing the executable binaries.