Depends on how you look at it. Lysandre wanted peace, and that's a very realistic desire. What's unrealistic is the means he was using to achieve it, but of course unrealistic means are going to be present in a Pokemon game.
Well, in a way. Grunts definitely interpret it that way, even if that wasn't exactly the main reason Lysandre was trying to commit mass genocide. He wanted the peace more than anything, and Team Flare happened to be the group that would benefit.
Of course he was. They all were. Except maybe N, who was just one of the most mind-numbingly oblivious people I've ever seen not to notice what the team he was technically part of was actually doing.
Speaking of which, at least the grunts this game had more realistic dialogue, focusing on (albeit extremely petty) goals like fashion instead of, say, Plasma grunts shouting "Plasmaaaa!" when they lose like they have Tourette's or something (I apologize to anyone offended by that statement, as I would never mock an actual human with the condition).