Thanks to the reveal of one of Zack Snyder's storyboards featuring Darkseid, and a little bit of context that this was a vision seen by Cyborg, we know that Superman's return was far heavier than what happened in the movie. Thanks to some leaked pre-vis footage and behind the scenes shots, we know his initial return and fight with the League was mostly the same, with some Superman dialogue changes made evident by bad CGI mustache removal, but the League had far more reason to fear him than that.
Batman has already had one "Knightmare" where he's killed by Superman. This new Knightmare by Cyborg has a reference that makes it in the final film when his armor freaks out at Superman and he says "it's more powerful since the interface" (referring to his interface with the Kryptonian ship, which trigged the Knightmare. The reason his suit would react that way to Superman is because he was just exposed to a potential future where Superman killed Batman and possibly more League members.
This means the fear of Superman would go far deeper after his return. There's clearly more missing there, as Superman's recovery and return to good ol' Clark (with a few more scary CGI smiles) is so truncated. With such a significant portion of Superman reshot, it's clear his part in the movie wasn't what Warner Bros. wanted. After both Batman and Cyborg had a dream about Superman serving Darkseid in an apocalyptic future, there was likely more mistrust and concern from the League after he ended up battling them in Metropolis.
The negative response to a conflicted Superman who has trouble gaining trust from the people of Earth - particularly Batman - was a clear influence on the reshoots, as those elements were absent from the final product, but it was a theme likely to be continued by Snyder, with the League slowly coming to trust him, eventually ending up in the same place as Whedon, only with a little more angst in the middle.
Collecting the Super Suit
We know from Flash's cameo in Batman v Superman that Lois is "the key," but we don't know what Superman's full recovery originally looked like. Joss Whedon's final cut removed the Kent Farm scene that seems to imply some more time spent there and a much deeper conversation with Lois. Whatever happens, though, he does accept his role as a hero again and return to the fight, only he has to get his suit first.
While the movie has him simply showing up in a brand new suit, we've seen the deleted scenes where he returns to the Kryptonian ship to get it. While it certainly functions as a small plot hole filler, that's not its sole purpose, as it's also a completion of Clark's arc, bringing him to the moment of choice where he chooses to be the bright beacon of Superman he was meant to be. Without this scene, the only thing separating him fighting the League in Heroes Park and him saving the day against Steppenwolf are a few short lines of dialogue about how Lois thinks he smells good and how coming back to life feels "itchy."
Without the infamous Snyder Cut, it's impossible to know exactly what all these gaps in the movie were supposed to look like, but it's pretty easy to identify that the gaps do in fact exist. Simply extending the plot from Man of Steel and Batman v Superman to the context of the known Justice League deleted scenes reveals that a good chunk of Superman's resurrection and return to the symbol of hope he's supposed to be were cut and partially reshot, leaving Justice League's Superman with a beginning and end to his story, but nothing to connect the two.