Every Mission has "Rules of Engagement". The rules of Engagement change depending on the Objective of the mission. If you're on a "Search and Destroy" mission, you have free reign to cap the baddies before they get you. A perfect example of the changing nature of rules of engagement is the Series "Generation Kill". They are told going on to an Airfield that the area was a "freefire" zone and anyone encountered could be considered hostile. While earlier, they were told shoot only when shot at!

If you are on a hostage rescue mission, the rules are different than they are on combat Patrol. I would think that Cobra, being a terrorist organization with a reputation for violence and the fact that they (unlike real terrorists) wear uniforms making them easy to spot, GI Joe should have standing orders to shoot on site!