On the topic of the virus bomb, it wouldn't be a moral dilemma if the genocide bomb wasn't horrifyingly tempting. It's kind of an ethical and moral test the QM has laid out for us as questers here: there is an option that feels very easy to us, that will resolve the issue, that as discussed is an expedient answer—but such an easy solution is also something that is morally horrifying, makes us recoil, to present the choice to the questers. Do we do what is easy, or do we do what is right?
But just as in real life, the option that seems easy and sacrifices morality and care for expedience will inevitably have inevitable consequences, which will force one to ask: even if one is willing to choose to do a great evil for the sake of ease, is that great evil truly worth it, or will it inevitably lead to even worse consequences down the line?
A theme in this story as well as in the source material seems to be that whenever in Helghan's history a "hard man makes a hard choice", when he chooses to do evil rather than take the harder, more uncertain path of what is right, that inevitably blew back on the Helghan people. The opening blurb of the story even describes that. Meanwhile, this story's take on Battletech seems to adopt as a theme that the endless cycle of paying evil unto evil, of inflicting easy cruelty only leads to a bad galaxy staying bad. Using the virus bomb would be to continue this cycle of cruelty and evil onwards the cycle that went from before the Succession Wars, but it is possible to choose not to visit more atrocity upon existing atrocity. Perhaps there's none of the easy certainty of the virus bomb definitively ending the war, but it's a start, to have the option to do the easy, expedient, and evil thing, and choosing not to do so, to choose to live in a galaxy where better things are possible. It'd be a difference from what happens so often in the source material.