Parece que o melhor caminho é bloquear o contato.
Neste link que aponta para um tópico na Comunidade do Skype, você pode encontrar mais informações:
in your case, you can temporarily block the contact/s whom you don't want to see you online. Blocked contacts will not be able to see the status on the contact that blocked them. Then you can just unblock them anytime you wish to. They will receive no notification or whatsoever when you block them, so they will be clueless that you blocked/unblocked them.
If you need to block/unblock multiple contacts, you can also place those contacts under a contact category.