The repo version simply downloads the binaries from the Skype website and installs them in the right places.
So, in that sense, there's nothing "special" about the package you can get from the repo. Whatever problems the skype binaries have will be there for the repo package.
The skype version of Linux is different from the one on Windows, so maybe one cannot instantly extrapolate from one platform to the other. Also, maybe it helps if you're running a secure system (not logging in as root, etc..), which tends to be easier or more common in Linux than in Windows.
A lot of the comments I've seen are somewhat paranoid. People see in their firewalls that skype starts all sorts of connections to other computers and get scared. But that is just how skype works and is probably the reason why it works so well.
Then again, just because you're paranoid, doesn't mean they're not after you...
I don't know what kind of things skype might monitor on our computers.... Skype is proprietary software, you cannot see the source code, and the protocol it uses is also not open. If that concerns you, you might want to try some open-source alternatives that use the sip protocol (I don't think we have any alternatives in the repos... somebody correct me if I'm wrong).
Perhaps unfortunately, nothing else I've tried works as well as skype... but that would depend on your requirements.