After re-watching the trilogy and reading this blog (specifically the "Love, Actually" part), I believe the answer is:
The <PERSON> could not understand her choice to help the humans end the war because it was an irrational choice based on becoming emotionally attached to them, counter to her original purpose
In the third film specifically, there is emphasis placed on machines effectively having "human emotions", most notably demonstrated by <PERSON>'s conversion with <PERSON> in Mobil Avenue:
<PERSON>: No. I don’t mind. The answer is simple. I love my daughter very much. I find her to be the most beautiful thing I’ve ever seen. But where we are from, that is not enough. Every program that is created must have a purpose; if it does not, it is deleted. I went to the Frenchman to save my daughter. You do not understand.
<PERSON>: I just have never…
<PERSON>: …heard a program speak of love?
<PERSON>: It’s a… human emotion.
<PERSON>: No, it is a word. What matters is the connection the word implies. I see that you are in love. 80
Can you tell me what you would give to hold on to that connection?
<PERSON>: Anything.
<PERSON>: Then perhaps the reason you’re here is not so different from the reason I’m here.
The Matrix Revolutions transcript
This shows that machines/programs are capable of forming "connections" that are akin to human emotions such as "love", despite being irrational. Sati was created without purpose, out of love, after all.
From the blog I link above:
These programs are experiencing a profound connection to each other, one that they're using the word 'love' to describe, since it's as good a word as any, and it shares a reasonably close meaning with <PERSON>'s understanding of the word.
If these programs are capable of "irrational" connections that are comparable to "love", then it makes sense that the Oracle has developed a profound connection with the humans race, especially since she's been studying them (that's why she was originally created, after all):
Architect: ... Thus the answer was stumbled upon by another – an intuitive program, initially created to investigate certain aspects of the human psyche. If I am the father of the matrix, she would undoubtedly be its mother.
<PERSON>: The Oracle.
The Matrix Reloaded transcript
She even makes the same choice again, according to this line, despite the fact that she cannot understand her choice:
<PERSON>: I made a choice, and that choice cost me more than I wanted it to.
<PERSON>: What choice?
<PERSON>: To help you to guide <PERSON>. Now, since the real test for any choice is having to make the same choice again, knowing full well what it might cost – I guess I feel pretty good about that choice, ’cause here I am, at it again.
The Matrix Revolutions transcript
"I guess I feel pretty good about that choice" doesn't sound like she understands it, but the fact that she's describing it as "feeling good" makes it sound more like an irrational "emotional" choice rather than the sort of logical decision we'd expect from a machine/program.
Generally speaking, it seems that the Oracle has come to value emotional connections such as "love", as we see her "teaching" to <PERSON>:
(Oracle’s kitchen)
<PERSON>: That’s it. That’s the secret. You’ve got to use your hands.
<PERSON>: Why?
<PERSON>: Cookies need love like everything does.
The Matrix Revolutions transcript
The "like everything does" part shows us that perhaps her understanding of purpose is evolving past that of some machines/programs (certainly the Architect), likely as a result of her studying humans and their emotional connections. Simply playing out one's purpose as many machines/programs isn't as important as connections such as "love".
I conclude that she must have somehow come to "love" or otherwise care about the human race, and then decided to help them, despite the fact that she did not understand why, since that wasn't part of her original purpose (which was merely to study them). Although she isn't an exile, she does essentially go against her purpose, against the system, but in secret, hoping that the outcome would be as she predicted, despite not being able to see past her own choice.
<PERSON>: Did you always know?
<PERSON>: Oh no. No, I didn’t. But I believed. I believed.
The Matrix Revolutions transcript 973