No, Ekiga is much worse, Skype is encrypted. We don't know who has the keys, but it's safe to assume that they're not handing them out like candy, since there are no reported leaks. Ekiga transmits in clear, anyone who can read your IP traffic gets the entire conversation handed to them on a plate.
In theory you can get encrypted SIP. But now you've gone from Skype (your grandmother has it) to Ekiga (your friend running Ubuntu has it) to encrypted SIP (you once met someone who knows a guy that has it) and there's no point having a communication network if no-one you're interested in communicating with is connected to it.