I wouldn't go so far to say he destroyed the characters but he watered them both down to the point where neither of the characters acted like themselves except in brief moments. It's not just about Superman smiling, it's about him having a viewpoint that is more positive than Batman, something the film fails to deliver.
The only way the fight happens in BvS is if both characters are not who they've portrayed in other media for decades. Batman can't be the world's greatest detective in this story otherwise the fight doesn't happen, and Superman can't be his more positive self in this story otherwise the fight doesn't happen.
Combine that with the fact there is no contrast between the two characters, and the cornerstone to any Batman/Superman relationship is their ideological difference. There's no inherent difference between the two characters, both are sombre and have a negative viewpoint of their world. On top of that they are both perfectly ok with killing people. Not only does that fly in the face of the decades long history between them, it's just flat out poor writing in general to have no contrast between two people who are suppose to fight each other. The argument between the characters is forced and requires you the audience to make the story meaningful via your knowledge of comic book history.
And lets be honest with ourselves, BvS is not a film with a positive viewpoint, in fact it drags its heroes through the mud almost in an attempt to show us how flawed they actually are. Is it any wonder why people disliked it? People want to see their heroes challenged, not beaten to a bloody pulp. You can't blame people for walking out disliking this movie when they feel two of their favourite characters have more or less been spat on by someone who claims to be a fan. There's making a serious superhero movie, and then there's making a dreary superhero movie. Nolan's films for all their seriousness are embedded with positivity despite its dark surrounding, every film ends on a positive note. Snyder forgot that. He was so fixated with what he wanted to do with these character he never stepped back and asked whether he should do it in the first place.