I thought Jack found out about Ascension Project through Shepard. She really did sound concerned about another Pragia and kids being tortured and I think she was at least curious at that time. She didn't get into Purgatory because she did anything really bad, she broke into Cerberus facility and saved a lot of people before she get caught by bounty hunters.She narrowly being made into another Cerberus test subject again if the mercs hadn't taken her in. She's more a victim of circumstance and if you're kind to her (mostly be neutral to her when it matters, don't try to fix her etc), she'll be more willing to change for the better.
I like to think that after her loyalty quest, Jack went on researching about Ascension Project and during Shepard's incarceration, infiltrated the station to see how the Alliance been treating the kids. She would have been caught by the security and Kahlee did a background check with Anderson and then her association with Shepard would have helped clearing Jack. And the academy already been receiving threats and infiltration from Cerberus themselves and who else would protect the kids better than the woman who hate Cerberus with every cell in her body.
Mass Effect is a bad choose your own adventure game. They did good about giving you an illusion of dialogue choices and alternate situations but a lot of stuff was pretty definite.