You don't call making a biological weapon to exterminate the Borg's enemies at cellular level in exchange for passage through Borg space butchering innocents for her own gain? All they did was have the audacity to defend themselves and included Voyager in that only after they tried tractoring, beaming away and boarding their ship and then were seen collaborating with the enemy that invaded them. Not that different from what Ransom faced. Killing beings to get his crew out of danger and closer to home.
I was talking about how Ransom justified the first space slug already being dead. I could easily see Janeway making the same justification... and it's a slippery slope once you engage upon it. What if the Krenim were still attacking and they needed two more to get past their space? Would she really say those two were worth the rest of her crew's lives? She twisted herself around so much with the Borg alliance, I could see her doing the same again very easily. She was already irrational in her decision making to the point of threatening to deactivate the Doctor, chewing out Chakotay for a birthday gift and thinking Voyager is conspiring against her.
As much as I poke fun at Janeway being horribly bipolar and inconsistent, nah I don't think she's evil. Heck I don't think Ransom was. I do think all three our our intrepid Starfleet captains(including Sisko since he was brought up earlier) have made dubious moral choices. Really if anyone we've talked about was evil it was that Max fellow. He seemed the most unrepentant about the whole thing.