First of all, I am sorry to hear that you feel that way about this article. My goal when writing about an application is to provide an accurate representation of what it does and the potential dangers that may be linked to it.
As mentioned in this article, there are some obscure aspects of Skype that are being investigated by the open source community. I sought clarification on a few points from Skype themselves but the company declined to comment. Maybe part 2 will seem more clear on this point.
About the license agreement, it is indeed important that you read it and understand it before going further. Should you not feel comfortable with it, it is indeed a wise decision to not install Skype on your machine. Maybe your legal advisor could have a look at it too?
If you have the time, could you post the lines that make you feel that way about the software? Maybe this would help shed some light on the issue. :^)