Starfleet doesn't approve of torture or the death penalty.What about the fact that Lessing's actions, along with those of the rest of the Equinox crew, could be considered attempted murder of everyone on Voyager? The courts are very lenient in cases of self-defense, and the police are given much leeway in what they can and can't do or say to people who are suspects of serious crimes (they can lie to them, tell them have evidence the don't have, etc.). This was a matter of life or death to Voyager and its crew, don't forget. What we might not accept in normal situations is often forgiven when we are under duress, and I think Starfleet would see this as one of those times.
What Janeway did wasn't self defense because at the time she wasn't being threatened. She was doing to to trying to extract information. Wasn't the Geneva Convention put in place to prevent such acts? Wasn't that why waterboarding and Abu Grave was such a controversy a few years ago?