I think in a number of games they are actually evil, but personally doubt they'll do that in FFXIV since the players would then no longer fit in with everyone else. However, it would be kind of awesome story-line where you shift teams "You're my only hope _____" Says Minifilla, meanwhile in your Dark Knight quest line you're learning terrible power from Ascians and setting her up with the bomb. lol. Still don't think they'd do that but, what a change of pace that'd be XD.
Also for moral relativism fun, just because you may see the Jihadists actions as bad - it would not empower your opinion any further than their's if only except in group think power where a system generally bound to popular opinion would vote upon the morality. So was it really a great evil of good intentions or a great good of good intentions (not that I personally see it is good of course, awful, but the fear of what moral relativism means is probably what turns a lot of people to forced structures)? Can you imagine if we had to start every sentence with "in my world view" :P. Although I try to "imo" a lot in the forums because it seems people when they disagree will try at anything to tear your personal character down.
I mean I don't mind a clash of opinions, but so often it turns into "you like grass, you must be an idiot" when you couldn't have just thought perhaps I have a great appreciation for nature looking good, that it was my opinion on visuals (which are like "blue is a good color"), and think that the quality (I could have proven this one) didn't match the rest of the game or its relative competition and I just wanted what I thought looked good and with a consistent visual narrative (there was a missing consistency, the idea that consistency is better of course is an opinion too though). Again, I think their 2.0 efforts were amazing and haven't even thought once to ask for a "fix".