The game itself operates solely on ethics, and not morality. It's a card game; it can not possibly have morals. The rules on the cards, however, creates a system of ethics if they're going to be followed. Players are the ones with morality.
To use some of the examples you gave, if someone makes a run, then realizes that they should have clicked for a credit beforehand, I'll make the call to let them differently in different situations. In a casual game, sure, take the credit! There's nothing on the line, and we're doing this for fun. In a tournament? Probably not. If there's no new information gained on the run (ICE is rezzed, you're reasonably sure the upgrade is an ASH, etc), then it's up to the player to correctly math the run out before making it. You're in a tournament, where the goal of it is to have the person who played the best win the tournament, and part of playing your best is to correctly assess situations, and to do the basic math before making your run. However, there's not much morality at play here. There's the slight nuances between what's expected at a casual game vs a tournament setting, but it's really on a pretty minute moral scale.
There was a game I saw viewing on Jinteki.net, however, where I think someone was morally pretty shitty. This was a situation where I think a takeback was correct, and it was interesting because it was the online setting that caused the situation to occur. A MaxX player was hammering R&D with a Medium installed, and had just Parasited the only ICE over R&D down before making a couple runs to see cards and build medium counters. On the corp's turn, they draw, instantly throw a second ICE over HQ, click for two credits (seeing as they were poor-ish), and pass the turn. The runner immediately runs R&D, seeing as it's open and he has a Medium down.
Here's the morality issue. The corp says something along the lines of "Oh, crap, that ICE was supposed to be over R&D." The thing is, the dude misclicked a button and didn't realize his mistake before passing the turn. This is something that would never, ever happen in a real game of Netrunner. Because there's buttons on J-net, though, it occurred. And the runner simply says "Successful?" The corp clarifies his position, repeating what he said. The runner says "Yeah, but you ICE'd HQ. Is the run successful?"
And that's bullshit. At that point, you care more about wining Netrunner than you do about playing Netrunner, because you're not actually playing Netrunner at that point. You're exploiting something that could never actually happen in a real game of Netrunner. And I think at that point, yes, there's an actual morality issue.
The sad part is that the person who did this is a regular poster here on Stimhack, which is shitty. The game of Netrunner can not have morals, because it is a game. If an issue like this - one that happens during a game of Netrunner, but falls outside of it - happens, then it is a moral issue, and it's up to the players to be good people. Be a better person, dude who did this. And everyone else, be better than they were.