QMs have said that they don't offer trap options. If using diplomacy and subversion weren't at all viable, they wouldn't be available. We're not going to make them buddy buddy with us, but defeat takes multiple forms. As an example, we've been promised a second action, not for defeating Zavok since he bailed, but for reclaiming enough territory and Arsenal Pyramid.
For subverting the Restoration, QMs have said that propaganda would primarily affect the younger people who have been less harmed by Eggman. Their leaders are a lot more beholden to popular opinion than we are. Infiltration with heroes that are not known affiliates of us, such as Honey through her shop, should create opportunities for subversion. And when I say subversion, I very much mean having them split apart and devolve into infighting, as GUN is. Maybe we make a group that's more neutral on us, maybe we don't.
Even if that doesn't happen, it definitely opens up sabotage options to make the military victory you prefer easier and/or less destructive.
I highly disagree with the view that other options only end in some form of bombing them to death. It's going to be how we do many things, but I don't think it needs to be how we do everything, including here.