Eh, I don't really see the comparison.
The article shoots down its own premise about Superman killing Zod vs. Captain America not killing Bucky by pointing out that they're completely different situations. By that point Cap had already neutralized the threat posed by the Helicarriers, so he could afford to spare Bucky's life. But I got no indication that Cap wasn't willing to kill Bucky if necessary to save civilian lives on the ground had he continued to prevent him from disabling the Helicarrier. He didn't want to, but he would have if necessary, and in fact almost did. Likewise, Superman had an ongoing threat to civilians both on the micro-scale with the family Zod was threatening and on the macro-scale in that the Phantom Zone was closed and no prison on Earth could adequately hold Zod, so he remained a threat to the planet. Superman clearly didn't want to kill him, but he had to.
Now, as far as your point, I think it's often forgotten that the Superman we see in MoS has only been flying for a matter of weeks at most when the attack begins, and had never encountered nearly equivalently powered beings before, not to mention so many of them. His inexperience leads him to not know his own strength when throwing Zod across the corn field, and allows him to get tossed around by the professionally trained Kryptonian soldiers. I don't think he was indifferent to the destruction, as witnessed by his telling people to hide, by him saving falling soldiers, by him preventing planes from being knocked out of the air, and by rescuing Jenny from beneath the rubble. He's simply never dealt with this many foes with this much power before, and he's inexperienced and overwhelmed. People say, well why didn't he lead them out of the city, but I think he was trying to do that with Zod, and Zod kept forcing him to stay within the city to stop him, sometimes physically throwing him back within the buildings. In Superman II, Superman was fortunate that his enemies all attacked one at a time and with really slow, simple to deflect attacks. This was a completely different animal.
Likewise, the situation with the Helicarriers could have been pretty devastating to Washington had they simply chosen not to remain hovering over the Potomac and Theodore Roosevelt Island. Frankly, Cap and friends got lucky on that score, especially when they all careened down into the water and fortunately right back into the SHIELD Triskelion which had been evacuated of all the good guys (hopefully). They were saved more by the plot (which, don't get me wrong, I loved) than anything that Cap and the team did, since they weren't trying to steer the Helicarriers to a safe crash site.
I'm sure after the movie, Superman joined people in mourning and rebuilding Metropolis. It just wasn't really relevant to telling his revised origin story, IMO. It's just assumed that he's not a heartless bastard who doesn't care that thousands of people just died (especially since he chose to save humanity over his own people and just risked his own life for them, despite their distrust and fear of him).
Anyway, the article just seems to want to pit TWS against MoS based on the flimsiest of comparisons because TWS is the new kid on the block, but then it undermines its own point, IMO. They're apples and oranges as far as I'm concerned. That being said, I preferred TWS over MoS, which I enjoyed a great deal too. But TWS is pretty damn close to perfection for a superhero film. At least until the next best one comes along to surpass it eventually.
As far as superhero origin stories that challenge the status quo and show our hero in a different light: I like them sometimes, just as much as I like more conventional takes on the characters. Which is why I didn't mind MoS. I don't think it deviated from his basic morality much, except for some of the things Jonathan Kent taught him, and even then, Clark was shown to disagree with his father's beliefs, even when he honored them when it came to letting him sacrifice his life to protect Clark's secret. But when the time came to step up and do the right thing, he did.
