The Skype accounts getting hacked so easily beacuse hackers were able to log in using an old Skype username and password combination for send spam links.
If you have linked Skype and Microsoft Accounts at all, then you should be safe to link and merge with the new process.
Once the two accounts Skype and Microsoft are properly merged, Microsoft creates a Skype alias to let you keep signing in with a Skype username. To ensure nobody can try to sign in with your Skype username, you can continue using this or disable it under the aliases preferences.
To log into your old account, attackers must know the email address your account. So, even if attackers know your old password, attackers cannot log in to send spam messages or messages containing viruses.