She was far too obvious to be anything other than a traitor, and that was telegraphed by the insane sequence where Roy assured everyone she's quite safe now because STAR Labs* installed some firewalls... She's super-tech from the 26th freaking century, so a comparable analogy would be a 16th century guy drawing a chalk circle of runes around your company servers to protect them from computer viruses and being surprised when they don't work.
* STAR Labs - Building insanely powerful, nigh uncontrollable, plot-devices for no appreciable reason since 1972