That first question is really the core of it, isn't it.
My sister-in-law is a staunch anti-mormon. She started out LDS, very active in her childhood and into her 20's. She went to BYU-Idaho (then it was Rick's). Then she went back east and her attitudes changed. She started sleeping around and all that crap and left the church and for a long time was very very bitter. It consumed her, the animosity she felt to the church and, in her words, the "devastating culture of guilt and shame" that ruined her life, tainted her relationships with everyone. We had some long, often painful, discussions of what the church meant to all of us (my wife and I and her siblings). I really felt for her, even while her siblings lashed out, since they were also dealing with some of the emotional issues from their shared childhood (if you look up "dysfunctional family" in the dictionary you get a photo of my wife's family).
Finally, after about a decade of this, it seemed almost overnight, my SIL had a change of heart. I got her to talk about it one day and what she said mirrored what you say here almost exactly.
Her change of heart was not coming back into the LDS fold, but rather, being at peace with her own belief system. She felt at odds with her family, and herself, and she realized it was not "their" problem, it was hers. What you described about feelings is EXACTLY what she said brought her peace. She had fasted and prayed and read the bible, wanting to find peace. She had an epiphany (her words) that, although the mormon church is ABSOLUTELY wrong, it isn't necessarily evil. It doesn't have to be viewed as the enemy. She said her feelings told her that the path she was on was ABSOLUTELY correct. She described "feeling the spirit" exactly how we learn about it in the MTC (no she never went on a mission). She said the spirit helped her forgive the mormons she felt set her up to fail in her young life (my wife confirms her ward was like this more than others, driving every little thing home as if it were another chain dragging you to hell with no hope of release). And she felt she received forgiveness from the spirit for the contentions she caused in her family. She has worked to make amends since then as well.
It very obviously brought her peace, as the discussions around religion do not get mean and ugly any more. She "bares her testimony" of the falseness of the mormon church, of the truth of the bible and the freedom and warm spirit and peace she felt after her long nights "pouring out her soul" to God, and accepting, and being accepted and forgiven by, her Savior. She says she knows God lives, and knows that the LDS church is not his church since the spirit whispered it to her so clearly.
The evidence in her is astounding, if you knew her. She is very outspoken and often puts her foot in her mouth (even today but much less so). This is in no way something she could fake. She was always so bitter it showed in her face. She could not be around mormons without making comments. Even in random conversation she would blurt out that they were going to hell and they are destroying their children and should go to jail for raising their kids in such a damaging environment. It was painfully obvious she was not living a happy life. She has been far happier since her "spiritual rebirth" (her words), and I would say one of the most spiritual people I have known. She shows long-suffering and charity in ways she never even could before. And it has now been over a decade.
She is now far more christian in her words and deeds than her (somewhat overly-pious) brother who has been in the bishopric and/or stake presidency for the past 12 years or so, since he was about 26. My SIL shows a true testimony of Christ far stronger in its outward manifestations than my BIL ever has. I would be forced to say that I think she truly had a mighty change of heart, and received his image in her countenance. And it was in opposition to the Church.
So did the spirit whisper the truth to her? If not, how do you explain it?
I can kind of relate to what your sister is referring to, some church leaders are absolutely ludicrous in their methods of guilt trolling. I've been pretty suspicious of local church leaders and the egoism they get in trying to mold the youth ever since I was a lowly deacon, so I consciously ignore when such a "guilt-troll practice" arises. But I do feel for other youth, who are trying so hard to be the best they can, but still get guilt trolled into thinking so poorly of themselves and the status of their salvation.
I remember having an interview with a stake president, I wasn't very fond of because of his guilt-trolling methods (he worked for the Boy Scouts of America, you do the math) , and he asked me, "Have you ever participated in Sexual Self-Mutilation?"

I mean if that isn't the epitome of hyperbolic guilt trolling. To connotatively relate *jerkin it* to ACTUAL sexual mutilation practices such as ****oral removal in oppressive Arab societies is INSANE! I feel for the youth of the church, because the church isn't in and of its self bad, but there are sure some egotistical dumbasses who probably shouldn't be in such a position of power.