The game suggests Beatrix has been thinking like this for a while. Its a pretty blind stand point to assume that she only started thinking of it NOW. That's not what's going on. What's going on is that this is the first time we see a PERSONAL Beatrix moment; Beatrix in privacy (or so she thinks she is; obviously she doesn't know Zidane and co. are spying on her) is not the same person she is in public. In public, she's gotta keep this heartless cold general exterior, lest she shows weakness. People know her as this invincible warrior, she's gotta keep that facade up. But when she's by herself, she can drop it and start thinking emotionally and what not. That's really what's going on.
The only reason it happens after Odin is cause, as I said, its the first time we see her. This is the first part of the game we see Beatrix when she's just being a person, not a soldier, and we finally are seeing "Wow, maybe she is human after all", which also shows that while Brahne maybe evil, not all her subordinates, loyal or otherwise, are. And unlike Steiner, Beatrix is showing logical thought in the idea, rather than just blowing it off entirely as "NO! The Queen has some grand scheme that I just don't understand, and its for the good of everyone! I trust that!" I believe she was actually more like "Something is wrong, but...I can't really prove it. My loyalties still lie with her, but I won't deny the truth." And naturally, later on, when she sees Zidane was protecting Garnet, and Garnet was put under a spell, etc., that was the proof Beatrix needed to finally pull her Heel Face Turn.
And...I don't think the Invasion was planned out by Beatrix, she just carried it out. Remember, Kuja was charged with a lot of Brahne's strategic related stuff, including supplying her with all the Black Mages. In the scene where he's introduced, Brahne's even asking Kuja for how to deal with Cleyra. Beatrix just carried the plan out, and the Red Rose scene showed she very much wasn't fond of her actions.
Also, don't forget this factor:
Beatrix is a human being; she can hold back if she wants too.
The Black Mages, who did *ALL* of the killing, were puppets and weapons of mass destruction. The only thing they knew how to do was KILL, and that's all they did do. She didn't exactly have control of that. Brahne just told her "Send Black Mages in", and all they knew how to do was kill. Beatrix and her troops did nothing. And its naive to think she could run in, undetected when the entire village is on alert.
Edit: Actually, lets look at the script!
This is right before Beatrix's first fight:
Kuja: "Of course, Your Majesty. I will present you a marvelous display
of my power. I am certain that you will be most pleased. I was
wondering if you would gather your troops near Cleyra. I'm
certain those filthy rats will retaliate in full force, and my
black mages may not be enough."
Suggests that the whole plan was Kuja's idea in the first place.
Following the battle, she knocks your team to their knees, and then mocks you. Brahne tells her to come. If it makes you feel better, then just assume Brahne told Beatrix to come with her, not to waste time. Brahne wants results NOW, killing 4 people wastes time when Beatrix had already just won.
Next off....look at how long the attack on Cleyra took. Again, its naive to think Beatrix could just run in there undetected and get out easily. If she could, why not waltz in while the Sandstorm was still up, when they had a false sense of security? Simply put...she couldn't.
Reading the dialog...again, another case of "I don't have time to waste, you guys are beaten and not threatening, I'm leaving."
I dunno...I really think you're just slamming FF9 for things so many other RPGs are guilty of. I mean, FF8 is a far bigger offender here (not that people support FF8 plot.) Why did Edea, whose possessed by Ultimecia, who wants Squall DEADED THAN DEAD to avoid dealing with the time-loop...spare his life? Its far greater "What the fuck?" moment here. If it was Seifer who did, I could understand, but Edeamecia had no reason to keep Squall and Co. alive.
At least with Beatrix, the whole "She's got morals and is human too, you know" thing fits and makes sense for why she'd spare people. Again, she had no reason to kill your team; her goal was just "Get Jewel by any means necessary." Curbstomping your team was enough to get you out of her way, and even if you did follow, she'd just beat you again (which more or less happens exactly as I stated. Beatrix isn't evil, and has morals. And again, her troops didn't kill anyone; it was all the Black Mages, who are under Brahne's control. Beatrix was just using the troops, and pretty much entirely as a diversion.