I was talking about Root here. But you are right, Root could have easily beat Martine because of what you have said.

yeah, plus from samaritan's viewpoint, it wanted a covert action in its overall plan to search for the machine. It would have been too obvious if samaritan just took over the company.

She was an assassin and a hacker before she became obsessed with the Machine. I think to be that, one needs some serious skills. Maybe they can give a flashback of how she got her skills, but dwelling on flashbacks of her as an assassin would need her story to align with the current storyline.

Samaritan is irrational and unreasonable. So when Khan started looking into why the company was buying too much fuel, he became a threat to Samaritan.