The document you are referring to is from 2005. It is no longer end-to-end encrypted. Microsoft not only can intercept your communications, but in fact stores them for 30-90 days per their publicly posted privacy policy.

http://www.skype.com/en/legal/privacy/#retentionOfPersonalDa...

(this apparently does not apply to voice calls, but either does the complaint that they are picking up URLs and visiting them).