Samus couldn't help but like Trudy's attitude. The hunter happened to make a living out of suicide missions. In a sense, the entire situation was just an extension of Samus' normal element, and like Shepard she knew that even though she had spent years fighting for a now destroyed galaxy, stopping and breaking down would be useless.

"It's not an ideal situation, but," A slight hesitation, "I am with Chief on this, Kusanagi. Besides, hopeless situations were never an excuse to stop in my line of work anyway." She may have stopped being smart at this point, but she still left a lingering feeling of 'I'm with you on this, but we still have our disagreements so don't expect this too often, Chief.' Maybe only he picked up on it, but it was there.