When talking to Commander Janek I only get the option to kill her, if choosing other conversational options the conversation loops. Is there any specific prerequisite to spare the Commander? I already couldn't spare the guard either.
I'm guessing some kind of diplomatic level or a specific role (doctors might trick the guard they're here to heal people). But there's no real indication that I lack something to proceed in that way and Janek's looping conversation is confusing. If my away-team officer would simply state "Captain, if you would have more experience in diplomacy, you might be able to resolve this issue peacefully." then I as player can understand I may want to grind my diplomacy up.