Humans are not distinctly rational or logical. If your charactercharacters were a vulcan from the Star Trek universe, their devotion to logic might shield them from some emotional backlash of their decision's down side. ...but they are not.
Making a decision which affects the outside world, comes with the potential for negative consequences for the decision maker, even when no direct cause is visible.
If your protagonist is a moral person, guilt over the damage they have done to others may haunt them. The memory of a previous decision's consequences to strangers may haunt them, even before the new decision is made.
If the protagonist is a loving person, horrific anguish can rise from causing harm to someone they love. Love is recursive, so the harm may jump through multiple hearts before reaching your protagonist. If the decision harms the spouse of your protagonist's lover's brother and the brother suicides over that loss, both your protagonist and their lover are in for more anguish than their relationship can possibly survive. If the brother is already in a precarious emotional state before the action, fear might prey upon the protagonist, even before the decision is made.
Ego plays into these kinds of situations as well. If your protagonist prides themselves on some attribute or strength of character; and if the choice which is to be made would contradict that beneficial self image, nebulous hesitation and anxiety may precede that actual decision. This anxiety may seem to have no source as the story starts, but slowly clarify as the decision approaches, possibly adding a powerful subplot to your story.
The trick to any of these possibilities involves the subtlety of their insertion into your story. You can't just tell the reader that something emotional is going on. Emotions, especially complex emotions are one of the places where a delicate writing hand can weave magic. "Show, don't tell" is never more true than here. It is okay if some of your readers don't understand why your protagonist is disturbed by the choice, as long as the rest of your readers are carefully guided to a place where they can understand and relate to how complex and perplexing it can be to live in our world where decisions often affect and harm others.