I will type plainly, I distrust some of her actions:
- How did Bob and Elle Bishop know that Peter would go to that hospital to drop Kentucky Fried Nathan off? Either they used an unknown Issac Mendez to make that determination or Angela Petrelli helped them, she said "The only future i've ever seen is the one caused by you" in The Second Coming, which points to the possibility that she helped them capture him and recommended that they lock him up to prevent him from causing any more disasters, the first time is a bit unfair as she was willing to allow him to be a mass murderer, which made him a victim of their plans. The second time, Peter lacked information on Adam Monroes full profile, which almost caused the viral apocalypse, the third time was intentional when Peter went back in time to prevent Nathan revealing their existance, Angela was being a hypocrite when she criticised Peter's attempts to manipulate events, what does she think she's been doing?!
- Angela using Darth Sylar to clean up Peter's and Elle's mess is like giving a paedophile a job in a school, dangerous and an disaster waiting to happen, she might find out that she made a mistake herself when she believes that telling Darth Sylar that she is his biological mother will keep her safe, Peter helped clean up her ****, she need to repay the debt.
- If she knew that Peter was going to explode, why didn't she somehow tell him to leave New York?
Let's look at the other side of the coin:
- Angela ordered the Haitian to leave Claire's memories intact, because she needed to remember and possibly because she didn't believe that Claire deserved to be violated like that?
- Angela and Arthur did things that they weren't proud of to keep her safe, was it because of her ability to regenerate or because they were concerned for her safety? If they weren't concerned for her safely, they would've taken her from Noah Bennet long before the events of "Genesis" for testing that "she would not be able to recover from" according to the Haitian (he probably witnessed Elle's "testing" and was speaking as a witness).
- She admited to both Matt and Nathan that she did what she did to make things better for them ("morgaging" her soul is a her way of putting it), this indicated that disspite her dark deeds, she appeared to have the best of intentions.
- If she knew where Peter was and wanted him dead, she would've told Bob to send everything they've got just before they got to Odessa or to Victoria Pratt before he got to her. She would not have send Matt and Nathan (she let matt read her thoughts to tell him to shoot Peter in the head IF he could not be reasoned with, implying that she was willing to have him dead as a last resort).
- In the outbreak timeline, she knew that Peter would be there at somepoint and that he would need to go back to prevent the outbreak from occuring, he was clearly her last hope to prevent the disaster as if she knew where Hiro Nakamura is and if he wasn't dead, she would've somehow enlisted his help.
We shall see if Angela can become better than Bob when in charge of the company, both in professional ability and in moral integrity, will she avoid the mistakes of the past or will she decay like the rest of her now dead associates (e.g. those who wanted either Peter or Darth Sylar to blow up), although judging from the patest preview, she is tipping towards the "amoral self serving scum" category and Peter might be warned about her by his future self (possibly when he is put back in his own body).