If you were doing cocaine and/or weapons deals over Skype, you'd be a moron and wouldn't last long. Depending on the jurisdiction, if ms finds out that some type of criminal activity is taking place due to spying on Skype conversations, they may be legally obligated to report it to the authorities.
You don't even have to look far for examples of how privacy violations can cause very real harm to people. Just some time ago, gmail was hacked (possibly by chinese government) and the emails of some chinese political dissidents ended up compromised. Do you know what happens to political dissidents in China? Then there was that thing in Facebook where a glitch or a change in policy or something made some woman's private information public, and the woman in question was in hiding from a violent ex-husband. And this is just the tip of the iceberg here.
Contrary to what the moron Zuckerberg would like you to believe, privacy still matters.
Let's think of the situation where you're eg. an atheist in Pakistan, where being an atheist can get you a death sentence. Or like you said, a homosexual in Uganda. The problem is not MS sending your private communication to your "enemies" out of spite. The problem is MS recording and possibly storing your private communications with your friends, communications which you expect to remain private. Maybe you need to talk to someone who's in the same situation as you, or just have to confide in someone about your situation, having to hide in a country that is hostile to you. Now that conversation has incriminating evidence about you, and it's not that MS might purposely hand it over to some malicious party, it's that the malicious party might get access to it regardless.
It's only a non-trivial issue if you decide to be stupid with your life decisions; it isn't hard to be a good person (no matter where you are)