The actual problem was not Skype stealing the focus. Skype just notified the window manager that it had some activity. Then Awesome WM showed the tag (virtual desktop) as having activity. But then the KDE Plasma panel still contained a list of the active windows. In that KDE widget the window with activity was changed and Awesome WM then put the focus to the KDE Plasma panel.
I removed the window list from the Plasma panel and was never bothered again.