Well, you kinda deserved it
Even the most virtuous saint can have a sinister streak. The important part is whether or not you actually act on those dark impulses. That's one of the things that make video games so interesting - you can have fun exploring your meaner instincts without worrying about hurting anyone, going to jail, or destroying anything important. But just because you're in a safe, digital environment, doesn't mean that there aren't any consequences to your actions.
Even when games give you carte blanche to run wild and destroy everything, there's still a good chance that the developers have snuck in some kind of morality to, erm, 'nudge' you in the right direction. Whether that means sending an army after you to punish you for your transgressions or just killing you outright, these games make a point to teach you a lesson for your evil, evil ways.
The Legend of Zelda
This is classic video game punishment that still has the power to mentally scar anyone who dares attempt it. Attacking those innocent, feathery Cuccos that appear throughout Hyrule will cause them to swarm after you in a frenzied rage, and the only way to get them to stop is to leave the current area. It's a staple of the series, appearing in games like A Link to the Past, Ocarina of Time, and even spin-offs like Hyrule Warriors. Luckily, one or two hits won't set them off - you have to be incredibly deliberate in your quest to draw their ire.
Metroid Prime 3
Samus Aran may not talk a lot, but she's generally considered a good, kind-hearted person, always showing up to save the day when duty (or a few dollars) calls. But Metroid Prime 3 lets you take a few potshots at one of its few NPCs milling about near the beginning. You can't actually hurt them, but if you keep it up, a little turret drops down to defend them from your senseless aggression. Blow that turret up, and another, stronger one drops down to replace it. Destroy that one, and an even bigger turret shows up, and kills you in one blast.
Chronicles of Riddick: Escape from Butcher Bay
Conversely, Richard Riddick is not a good guy - hence why he's locked up in the hardest maximum security prison in the galaxy in the first place. In fact, Escape from Butcher Bay is perfectly OK with you killing off other inmates, as long as the guards don't catch you in the act. Well, that's the case in the first two sections of the prison. Once you make it to the super ultra maximum security area, any attempt to murder your fellow inmates will result in an immediate "death sentence" flag by the computer, and poison will instantly start to course through your veins, thanks to the cryogenic suit you're forced to wear. Human rights? Not so important in the far reaches of the galaxy, apparently.
Shadow Warrior takes the "retribution against animal cruelty" to a whole new level. Most of the creatures you can eviscerate in the 2013 reboot deserve it, as the only thing that doesn't want to kill you outright are some bunnies you'll see milling about and *ahem* getting amorous with each other. Try to interrupt their lovemaking by shooting them, however, and suddenly these innocent rabbits start hunting you down with lightning-quick speed while heavy metal blares in the background. Lesson learned.
Conker's Bad Fur Day
No one likes a team killer, but Conker's Bad Fur Day's multiplayer modes will actually call you out on your indiscretions. Take out too many of your own teammates, and you'll be branded a traitor. Soon, you'll find that there's nowhere to hide, as your AI compatriots will hunt you down until someone finally kills you. The final insult comes as they shout things like "Fucking traitor!" as they pump you full of lead.
The Badi Dea (say it fast) is a Star Destroyer that originally showed up in the classic space-sim X-Wing. The name is a hint; you're supposed to run away from this behemoth as fast as you possibly can, before it and its endless waves of fighters shred your ship to bits. But in the semi-sequel TIE Fighter, the Badi Dea is one of your allies - unless you decide to take out one of the ships you're supposed to be protecting. Apparently, the Empire considers this to be treason (with good reason), and sends the Badi Dea after you. It won't stop until you've been pounded into so much space dust.
Metal Gear Solid 2
Many games don't like it when you attack animals with wanton cruelty, but Metal Gear Solid 2 is one of the few to actually try to make you feel really guilty about it. Once you first climb out of the depths of the Big Shell and into the sunlight, you'll notice that the sky is filled with seagulls - who are more than willing to take a crap on you if you stand in one place for too long. If you spend too much time getting revenge by shooting them out of the sky, you'll get a call from the Colonel and your girlfriend Rose, asking you, in so many words, "What the hell do you think you're doing?" You can't even save your game until you apologize to Rose. You know what you did.
King's Quest 2
Half of the fun of those old King's Quest games was trying to outsmart the text parser by typing in random stuff and seeing if the game would do something with it. In some situations, it actually would - usually with hilarious results. If you walk into the church in King's Quest 2 and type in 'kill monk', the game actually throws up its hands in disgust. "Anyone who would kill a man of the cloth doesn't deserve to play this game. Therefore, we will end it," the game reads, promptly killing you dead on the spot. A simple "no" would have sufficed.