The solution is easy enough - just split this category into two different categories:
- "libre"/"free software" - holding software that is, in fact, Free Software (i.e. meets DFSG: http://en.wikipedia.org/wiki/DFSG
- "gratis"/"free-of-charge" - holding software that is free of charge.
Or, even better, make those non-exclusive, so that Skype would only have the "gratis" markings, and Ekiga would have both "libre" and "gratis".