This is really well-written, and I understand a lot of your points. I do respectfully disagree with your position on this topic. I know that the world we live in right now is a volatile, ugly place, but it is still my personal worldview that violence is (99.9% of the time) not the answer. Even when it feels justified, it alienates people from your cause, and ultimately hurts it. On a scale like this, collateral damage is inevitable and invalidating to whatever justice you're trying to enact. I disliked Flora the second we met her, when we saw her hypocritically setting off her sort of corruption bomb Darchlight Forest. Are your really restoring the Badlands if you're destroying the earth somewhere else? I think in many ways this gets into the main theme of the game--whether it is ethical or right to sacrifice the life of one for another, or many (in Flora's case, sacrificing life on one part of the planet for another part of the planet)--or, if it is better to find another route altogether (do nothing, wait for a phone call, act as a rebel, etc.). Even if her original intentions were pure, when she took on the role of a terrorist leader, she made a lot of irredeemable decisions. Don't forget what she did to Rune and Huey. I'm just saying that I think the point of this game is to say that things don't always have to be black and white, and there is always another way to go about things.
I think that, in terms of Bladestar, as you mentioned in your last couple of paragraphs, we should hold out for future releases though. Jan has implied heavily that we're not done with Bladestar yet. There are still working members, with Jenkel and V being at the top. There is still so much mystery surrounding these two and hopefully more will become clear soon. I think what Jan did so well was making Bladestar such a complex organization, and creating these questions to debate in the first place. Even if the cause was right, I don't think you can disagree that what Flora did was undoubtedly wrong. But, in terms of Bladestar as a whole, I don't think we should condemn the plot or characterize it with a trope until it's finished. I just think there's a lot more to this commentary on extremism than meets the eye, and again we'll just have to wait to see what route this takes.
I think another thing to consider is the role of the player character in this story. It's kind of an interesting phenomenon. While technically you are you, and make your own decisions throughout the game, there is simultaneously a definite role and personality that is already laid out for your character the minute you start the game. They are the Interceptor. They are meant to act as a balancing act between good and evil, darkness and light. They are the Zygarde to the clashing Xerneas and Yveltal. If you remember Adrest, the name of this character is very likely to be a reference to Adresteia, which is an epithet for the Greek goddess Nemesis. Her role is literally "the goddess who enacts retribution against those who succumb to hubris" (source). That is, by definition, a position that would be against Flora's role. In my opinion, Flora and the PC were destined to clash from the beginning, and it doesn't make sense for a character who is supposed to be of balance to join an extremist group.
That's just my thoughts. Again, really well written and interesting analysis. I just think you should consider waiting to pass judgment until the entire story is revealed.
In addition to my points above, I wanted to say that I think that the option to "join" Bladestar is presented to us in order to learn more about the organization (or story as a whole). If you choose to join them, you get to see their base and speak with a lot of members. You learn more about Flora, and learn that she is afraid of the Xenpurgis. I don't think the point of it was ever to derail the plot and work for an organized group. I think it was just an interesting way to learn more about the world.