You don't, mostly[1], lose freedom by installing Skype. You lose freedom by becoming reliant on Skype, and by installing (and using) Skype you are putting yourself at significant risk of that.

[1] You also may lose some control over your system, which may limit your freedom. At the extreme, consider malware. Recent, relevant Dilbert comic that I assume is an exaggeration: http://www.dilbert.com/strips/comic/2013-11-06