I think I may have the perfect solution.
Does anyone remember the scientist towards the very end of the earth portion of the game? the one that opens the door to the portal chambers after you kill off a couple Alien Grunts? Modify his script so that if you’ve killed any scientists, he won’t let you through.
The best part about this is that if your son has been killing off any scientists, he’ll have to either reload all the way back before he started killing them, or start a completely new game if he doesn’t have a saved game from before he started doing that.
I’d think this would pretty effectively drive home the “actions have consequences” ideology. Plus it’s more realistic, and prompts you to think ahead, as not all actions have immediate consequences, but severe actions such as those often result in severe consequences, such as not being able to finish the game, that you can’t simply go back and fix.
you would also need to make sure the game differentiated between deaths caused by Gordon and deaths caused by enemies.
I dunno where that specific script is though. You may want to write to valve and ask if they would consider releasing a quick update for this purpose, or at least pointing you to the proper script to modify. They’ve done crazier stuff and the worst that can happen is they could tell you no.