"Free software is a matter of liberty, not price." - Richard Stallman

So to understand the word freedom in the context of free software, I tend to lean back towards liberty as a philosophy question. What freedom means, is a question famous people have pondered over for ages. So to ask a single simple question if Skype gives freedom, here is a quote from John Locke:

"Persons have a right or liberty to not be subject to the inconstant, uncertain, unknown, and arbitrary wills of others."

Since the developers of skype can subject their users to any number of inconstant, uncertain, unknown, and arbitrary decisions, like including the NSA as secret listeners to private communications, Skype can not be defined as providing liberty.

For more details and guide to more reading: https://en.wikipedia.org/wiki/Liberty