No. As I already said, humans aren't gods and aren't considered to be pure good. Gods have godlike powers. They might not be omnipotent, but they shouldn't have to choose the lesser of two evils if they are actually good beings.
By no stretch of the imagination is genocide a good act. Even if every single living creature in that area was terribly, irredeemably evil, it wouldn't be a good act. It would be an evil act for a good cause. And in reality, no, not every single living creature in that area was irredeemably evil.
In D&D terms, it was a very major alignment violation that should have shifted their alignment to neutral at best and evil at worst.
This is a partial fix. The greater fix would be to either stop listing these gods as gods of good/neutrality/evil or to actually have them act according to their alignment.
So, in your argument, no good god can ever handle the Trolley Problem? That any good god faced with a situation where all options are bad, and it's a question of doing the least evil, that god can never, ever be considered a Good god forever afterwards?
Basically, you're arguing that all good deities in D&D are 1e style Paladins with an antagonistic DM who delights in making them lose their paladin status. Because there are lots of times when the lesser of evils is the only choice. And, additionally, since D&D deities are most specifically NOT omniscient, then they can be mistaken.
But, again, I have to ask, who considers the Cataclysm to be a good act? It might have been the right one (and we can argue that for a long, long time) but, AFAIK, no one ever calls it a good act. No one claims that the Towers of High Sorcery are good. Necessary, but, good? I don't think that's ever even suggested.
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Just a point too about the idea of remakes and reboots being bad. IMO, the question isn't about whether reboots are good or bad, but whether or not they are good or bad at a different rate than original works. Thousands of English language original novel length genre works have been published in the past year. Last statistic I saw put it at about 3000. How many of those are "good"?