My impression from their interaction when Stark is strung up was that she was asking him for what his note meant. Perhaps my interpretation was wrong, but her problem back in 1999 was essentially the same one in 2013; remember, her plant overheated and blew up. Stark denied memory of writing the note (something along the lines of 'The night, I remember. The morning after, not so much.') which seemed to be an implicit acknowledgement that his not was indeed key to their problem. Whatever, this is a lot of analysis for a shoot-em-up film.
I just don't see your reading of the botanist to make much sense. If she's genuinely an amoral person as you say, why would Stark's two minute diatribe have been enough to change her actions so drastically? She literally threatens suicide just to let Stark go (note she still is planning on working with Killian; otherwise the suicide threat would be a moot point). That's a pretty selfless act for the person who two minutes ago was working with the guy planning global domination.
Lastly, I certainly got the genesis of the plot - the veteran test subjects who couldn't 'regulate' (whatever that means) and blew up accidentally. What I don't get is why he even bothered doing this elaborate cover-up - it seems like there was little to connect the blasts to AIM, so why invent a terrorist persona at significant risk for precious little gain? And then going from 'we're going to make a lot of money' to 'we're going to make a lot of money, but we have to manufacture a terrorist threat to cover our asses' to 'we're going to make a lot of money, but we're going to take over the world while we're at it, playing fake terrorists against a fake government' in the space of ~6 months seems wildly implausible. They tried to frame it as some life-changing event from 13 years ago that made him go bad, but his only really bad actions seemed to happen compressed right at the end. I just don't get his motivation at all; he could be fabulously wealthy (yes, and powerful) with this technology through completely legal, relatively risk-free means... so why go through all of this convoluted trickery?
I don't think the movie was confusing at all - I had no trouble filling in the blanks they wanted us to. I just didn't buy it.