I’d go with it - as you say, it’s a common trope within the established stories, and is prime fodder for roleplaying. If the players handle it well, then the overall success of the mission should negate any downside for not following directives to the letter.
Also, a lot of directives have some room for manoeuvre: the commanding officer (or the fleet commander) could use their influence to get some negatives excised from the record.