Skype is safe to use; it might have been something unrelated, or a download of Skype through a non-official website (by accident, perhaps?) that is alerting your Anti-Virus of a trojan or infection. Maybe a KeyGen or something similar?
I've noticed that Skype and MSN are thoroughly integrated now, but by registering at hotmail.com for an e-mail, you can still use MSN messenger through the mail function on the left-hand side. Otherwise, there are mirror downloads on third party sites, or websites like ebuddy which can still connect to the host and function as an IM properly.
Otherwise, I am on Facebook, but that's a last-resort deal.
Wasn't sure if male or female, due to RMS saying you're male, but FIRST's profile says female /derp
Worst comes to worst, FB.