The Soldier Mentality
Rip loathes being in charge. Physically detests it. Keeping tight to orders and a routine keeps her stable, on track, and protects her. Disrupt that routine, and she becomes lost and confused, unable to find her way. Being independent forces her to think on her own, and she must then place trust in herself, which is not easy to do when you're a self-proclaimed monster. Trusting in superiors and following the orders they give allows her to trust absolutely in the system, giving her a sense of pride and purpose. Without orders, Rip would be forced to ask herself, "Who am I?", and many of the answers to that cause her to cringe.
Hence why she despised the idea of becoming an Angelii. While it made her more powerful and an asset to her cause, it was unfamiliar responsibility and becoming one of the first Angelii was even worse; she felt as though she was going above and beyond what her rank called for her to do. This horror was alleviated by Megatron's ascension as well, but in no rightly-governed universe should Rip have ever achieved the same rank as her recognized leader.
She eventually came to accept the Angelii position because it allowed her to look after and organize her "troops"; Rayne, America, Larry, Kid Flash, etc. These were people she felt inclined to fight for, and putting up a good fight in an upcoming war was an acceptable answer to an otherwise gut-wrenching position.
And now, it's very likely she'll transcend again, but this time the circumstances have changed; instead of using her new-found powers to aid her superiors, she's going to be using that power against them. What she only had the idea to do, she has now been given the means to see it accomplished. With it, comes the fear that she might actually survive her betrayal, and worse; become self-sufficient and able to protect her own without help from an army.
This is her greatest fear.
All of Rip's self-definition comes from army life; her loyalty, her resolution, her blood thirst and vampirism, her devotion and love for Germany and her political ideology. All of this she owes to her position in Millennium and later to the Decepticon forces. Show her she doesn't need protection any longer, or that she has a duty to rise above her chosen ideology, and you've thrown a wrench into her mental gears. Half of her wants to be a pawn or a lowly but loyal soldier, and the other half wants to give into hated ambition.
But mostly - and this is chiefly worrying - she doesn't want to evaluate her life for fear she realizes the potential deep within her, to be something more than what her bosses deemed her importance. Admitting that her commanders were wrong about her is akin to seceding from her position permanently. And after dying time after time, her position may be all that she has left.