The thing is, I think the scientists were complicit in Britannia's activities, so the argument can be made that they were asking for it. The really serious moral problem lies with the Geass-empowered children, who were just being used. Now Geass was being used to fight back in that one scene so maybe there was no choice, but was that universally true? What's more, given Jeremiah's Geass Canceler, it could've been possible to subdue them. Of course, true to form Rolo just kills them all, threat or not.