Also, don't forget, Siuan herself was the one to figure out that the Black Ajah KNEW Rand had been born and what they were trying to do about it. If the Black Ajah already knows, than the only people Siuan is keeping in the dark about the Dragon's Rebirth are the good guys! She is not protecting Rand at all, since the Shadow is fully aware of him. She is only keeping him a secret from those who might want to help him! Siuan, as far as she knew, was sharing a secret with the Black Ajah! Why do you do that? Plainly the Shadow is okay with keeping Rand a secret from the world, and as Moiraine says, is there a better reason to oppose something?

But in a manner that does not redound to her credit. She was wrong about the consequences she predicted for LTT's plan, after all. "No one anticipated the Dark One's counter-stroke" is the official word. And even knowing about the taint in advance, a strong case could still be made for going forward with the plan anyway. The Breaking was a preferable fate to the conquest and triumph of the Shadow. Latra Posae screwed up by allowing the Breaking to happen on her watch. Given what we know of her behavior prior to the Strike on Shayol Ghul, I would not be surprised at all to learn that a large part of what allowed the Breaking to happen was the same hesitant, dilatory & overly cautious, George McClellan-esque approach to a crisis. I am sure she dithered over the problem of what to do about the male channelers just long enough for them to escalate into a nigh-insurmountable problem.