Microsoft recently confirms that in their recent Skype versions from last year, user cannot disable by menu or bypass the auto-update.
If it happens to your domain users in your organization and refusing this Upgrade pop-up effecting Skype not to run, you need to follow these steps to solve it:
Step 1: you first need to completely Uninstall Skype from his PC through Programs and Features.
Step 2: Download last Skype classic version from this link (it not appears anymore on official site):
Step 3: Install the classic version and ensure it’s not newer than 22.214.171.124
Step 4: Before you launch it and login the account, you must open Services (as administrator) and set ‘Skype Updater’ to Disable
Step 5: Login your account and now you have permanent Skype without prompt for credentials every few days.