Thanks again for the feedback, folks. I've had to sit with this for awhile, especially considering multiplayer, but in synthesizing the ideas here I like the idea of "warning shots" that don't fully disable you combined with a tone and context-sensitive "surrender the goods" pop up icon. It would probably be smart to swap out parts of the screen for comms or cargo surrender rather than pop ups, as well. Since everything's mouse driven (joystick with menu selection via hat optional) it should be quick and intuitive if such icons always appear in the same place.

With people walking around I still don't have a good resolution. One thing I'm thinking about is a "Caught Flatfooted" status effect that ties in with stats like Perception and stealth. If your character is so surprised that they're not able to instinctively react, they raise their hands in surrender. Maybe this doesn't occur if your character has a weapon in hand unless the enemy either has a weapon or tactical position (gun to your head) that would instantly kill you.