I'm not big into the theorising side of Deltarune, so I don't know if I'm missing a huge amount of information or if I'm saying something blindingly obvious, but I cannot see a world in which The Knight's plan is to intentionally cause harm.
While it's methods are... Certainly enigmatic if you take this into consideration, and I don't have an explanation for any of it, I just feel as though everything we know about the Knight struggles to line up with the idea of them being a completely malevolent force.
First, let me point out what's right in front of us. In the main quest of the game, that is to say, what you'd see if you were playing without delving into any of the secrets, it is quite literally a "Knight" bringing townspeople into a "shelter".
This could be used to subvert expectations, but I doubt it. The Knight has been presented as the antagonist since CH1. What makes the most sense is a subversion of expectations the other way. Despite the fact that, to Susie mainly, the Knight has been shown as something that needs to be stopped, most actual descriptions of the shelter seem to have an overlooked other side to them.
In CH4, Alphys tells Kris that it was originally built to protect hometown from danger and in the same pre dark world sequence, Ralsei comforts Susie by telling her that if the Knight wanted to harm anyone immediately, it would have by now.
It's also worth mentioning that the prophecy panels hardly even allude to the Knight as far as we're aware. All it does is vaguely say that it will "duel the heroes", which we... Already know. A figure so huge in the world of our protagonists is hardly touched upon in the grand scale of the prophecy, especially compared to the Roaring.
Next, let's take a leap and assume the Knight is Dess.
Dess, who belonged to a highly regarded churchgoing family, who's the sister of one of the most major characters in the game, who hides military rations in her room, who's working with Kris (Asgore's child!!), is now forcefully bringing people with close ties to her family into the shelter intended to protect the people of hometown.
Based off of this information, my assumption is that she's trying to prepare people for the Roaring before it happens. I don't knoooow. A hole can be very easily poked through this, with the fact she's making the fountains that are causing the Roaring, but considering the religion this world seems to follow presents it as something inevitable, it could then be argued that she wouldn't care if it happened or not? I don't knooooow.
My last card to play is that we know there is a Dark world in the shelter, and that especially after CH5, the narrative is trying to present the existence of Darkners and Dark Worlds as something that doesn't have to be bad (however flawed Flowery's argumentative... Skills were), it doesn't feel right that the shelter dark world would suddenly be uniquely evil.
Come follow me into the dark or whatever.