And why would you want skype on the phone without contacts??? You can easily delete your skype account and your problem is solved.

Don't know for google but for skype I would say definitely NO.
Your skype contacts actually are not saved on any device, only on skype server and you see them each time you log in because device you are using gets synchronized with skype server. And this makes perfect sense. Any other way would make your life very complicated because you would have to sync skype contacts across several devices all the time.
And I don't see problem here. I merged skype contacts with those on the phone and that's it.
Or you can let them as standalone contacts but set your phone book to sort them by availability.
Or try to merge all your skype contacts to one called skype. Haven't try that so it might not be possible.