I'm sure it is possible, but keeping it from breaking with every release is going to be tricky.
Plus one of Skype's benefits is that it works on "everything" (Windows, Linux, Mac, Android, iOS, etc); so your solution is only as good as the platforms you can tag.
You could as well use an external tool to en/decrypt your text with for example blowfish + base64 encoding and use Skype just as the transportation layer of the encrypted messages.