Where does she get all that stuff anyway - guns, clothes, equipment - if she's in prison? Which also raises the point - if she can escape any time she wants, then why does she stay?
That's another part of her character that I like: she's very intricate. I think she stays because she does feel personal regret for whatever she did and feels that she deserves to be punished for it, but that doesn't stop her from leaving if she's needed elsewhere and/or by The Doctor. But then she goes back, to finish the rest of her sentence. (I think she probably went back at the end of TBB and hid the vortex manipulator in her cell, which was how she was able to leave after getting her letter in TIA.) And of course, if my speculation is right, then she could have a house/condo/apartment/secret someplace where she has all of her stuff that she'd need access to when and if she does need to escape the Stormcage.