Marvel movies should not be judged by comic book accuracy as it’s not a live action version of any specific comic. They are based on the comics and can be considered a separate universe like any different version of their characters in comics.

I think this is pretty fair, but when it comes to something like Supergirl, directly adapting a story that the team has talked about how much they like, massive changes are worth talking about

I agree with this. I think as long as they are true to the character, the plot doesn't necessarily have to be pulled directly from comics.