I don't think what you did wrong is the same as what you think you did wrong.

Let's say I believe you, that the lie he told the princess was absolutely the worst lie he could have told. Did you have him roll for it? It doesn't matter if it's implausible if someone believes it. Besides, on a good roll, maybe she doesn't believe the bullshit story, but that doesn't mean she has to let on that she doesn't believe it. Maybe she just wants to see where he's going with it. She doesn't have to call the guards right away. Sure, she's putting people at risk, but if she thinks he's genuinely not a bad person, she's might take that risk. Even if he's obviously lying.

Also, completely on a meta level, who cares? Let me start by asking you if you made him actually try to hack a computer to have his character hack the escape pods? No, of course not. His real life ability to hack computers, or shoot people, or lift weights, or anything really isn't relevant, because he's not in the game, his character is. Yet, his success or failure at lying is decided by his real life ability to come up with a believable lie. Not only that, but he's creating a lie that is supposed to work in a universe that he doesn't exist in. He doesn't actually have the life experiences of his character to help him think of a good lie in that moment. Not everyone is good at coming up with things on the spot. And you know what? Next time he's not even going to bother. He knows that making what he thought was a reasonable attempt just leads to his character being railroaded to a horribly un-fun death.

So here's the thing, you did basically what most of us do when we start out, and that's be too hard on the players. They aren't the brilliant improv geniuses that we'd like them to be, but that's okay. If you let them get by with shitty lies now (maybe let them know that other lies would have made the roll easier), it will at least let them have fun lying, so that they will do it again, and hopefully improve over time.