First of all, the story is not just about the MC, it's about all main characters and the most "main" of all main characters is Ellie^^
Second: There won't be any bad endings, there will be consequences and you can lock out some charaters, but there won't be a straight up bad ending. This game is all about forgetting the past and heading towards a great future, not the opposite
The choice you have with Ellie in "that" night wasn't even planned, it was just a potshot at all the people who didn't understand that the story can't progress without having certain things happen.