The wilted rose image was NEVER meant to be an imagery of SA happening?
Alright so, I now kind of want to talk about the change a bit more seriously:
I think that the cornerstone of any discussion regarding the change should be a very simple fact: Chapters 3, 4 and 5 were meant to come out in a TANGENT!
Chapter 5 provided more context on what the flowers symbolise in Deltarune's lore: fair and expected enough, they are the markers of dreams and love!
The wilted flower imagery is still valid, for this same reason! The red rose is a universal symbol of love at its most passionate, and Noelle does hold very strong love for Susie... But also, for Kris as well. Noelle has been pining for Susie for quite some time, but also she yearns to reconnect with Kris and SHE is the one that initially leans in for a kiss with Kris in the couch scene!
...a kiss that Kris denies. Perhaps, because of knowing it weren't really them that allowed the things to come to this point. Perhaps, because they actually like Susie. Or, perhaps, because there were some things they felt compelled to "show" to her.
The scene in Chapter 4 gets quite literally lit up with the red, and it is also important. The red light in Deltarune's setting is the marker of connection with the "divine beyond"! It is the Red human SOULs that are so far the only ones proven to be connected with the Player, it is the color marker in which Carol addresses YOU (again, the Player), it is the light in which Kris' eyes glow when they are opening the Dark Fountains, EXP and LVL are also red according to Sans and they're the stats in which the Player erases Kris and creates a "Chara". Needless to mention that during Weird Route, Kris gets similarly "erased" by Player's influence as Frisk once was! Just remember how the narrations upon checking here and there in Chapter 5's Weird Route became 'blank'!
Toby is not shy of addressing dark topics in his stories, but in this case I would say the intended message is that Kris somehow was able to "show" Noelle the beyond. As plain as it would be, I think they could simply pass her the knowledge through their eyes. For example, Spamton, who was also ruined by seeing something he was not meant to see, reported seeing something so bright that his eyes were burning!
So, why the flower wilting? As a marker of the things that were meant to flourish but now never will!
Noelle's love will never flourish now; her crush on Susie becomes meaningless in the comparison after what she has seen and her born-anew crush on Kris got harshly rejected literally as soon as it appeared! Noelle's dreams will never flourish now either; she already had very little to hold onto earlier due to her mental state and now completely resigned to just "leaving". Regardless of what you believe happened in the lake, she does not believe that where she and Kris are going is JUST death. She is fully convinced that they are going somewhere "real", away from the artificial world of the videogame's bounds. Much like Jevil once have, she deems everything worthless now.
The thing is, this imagery IS quite hard to decipher without the provided context from Chapter 5. There was a miscommunication of what intention Toby really wanted to convey due to a lot of things missing, so fans commonly interpreted it as 'wilting rose = "defloration" = sexual assault'. Not unreasonably so, either: Chapter 2 of the Weird Route literally had 'marriage' symbolism and themes of coercion and... well, characters were literally on the couch, right?
But the very fact that Toby removed the wilted rose proves that he was NOT happy with this becoming a widespread assumption! Toby is not... particularly cowardly when it comes to being questioned. HE of all people would not worry about Twitter users interpreting him as a weird creep for allowing the players enact a SA scene between two teenagers, for two reasons. One: many people thought something so dark was powerful and interesting, the presumed backlash wasn't as bad. Two: Toby is friends with several "problematic" people and is strongly against censorship in fiction and fan creativity. Forget "Toby chickened out and decided to be toothless", he is not this type of writer.
The only way I see him worrying about the reception is only if it was wrong to HIS vision! There were similar instances of Toby gently pushing the fandom to understand better with the morality of his characters! For example, he had to add a dialogue for the Spade King to clarify that he was as nuanced and sympathetic character as everyone else and addressed Chara being "sweet little chocolat" that Asriel DID love dearly on his OWN accord without any brainwashing on his streams, as a response for the fandom portraying them as pure, irredeemable, one-dimensional evil in its highest form.
As for "what was he even expected?" question? Again: in HIS mind, Deltarune existed as a whole, and when he was including the wilted flower scene HE had Chapter 5 in mind, unlike us! Besides as a fellow writer that contains 500 terrabites of not spoken out loud lore in my head I can testify that you can and WILL get tangled in your creativity to the point it becomes harder to tell which one of your thoughts are self-explanatory and which require context!
Unlike the flower imagery, the connection between the glass and broken dreams was already foreshadowed since Chapter 2. And so, replacing the flower with the broken glass was an arguably better way to connect the Chapter 4's scene with pre-established symbolism and what was MEANT to be conveyed!
In retrospective, broken glass imagery works very well: Noelle described her apathy and depression as "looking at herself through the glass" and now that she finally saw a VERY bright and solid goalpost above everything else, that "glass" cracked. But at the time before Chapter 5, the only way to give fans a hint was going with 'you know, fallen star cried and its tears formed a glass, glass shards are formed from broken dreams and now we are destroying Noelle's dream about having meaningful connection with Susie and just salvaging something from simple things in life! you know!'.
Glass imagery is the only way to properly connect overarching symbolism whereas needing to keep the message itself but also account to the missing Chapter 5's important insights! I fully believe that rose imagery would be kept had Deltarune came out in full at once, or at least had Chapter 5 came out with 3+4 bundle! What can I say? Development issues can cause debatable changes sometimes!