You probably feel bad because you know you were doing the right thing, yet what seemed "right" still had a negative impact at the time. You shouldn't feel bad, because I assume that the person who made that decision is not a close friend, therefore this decision will not harm any existing relationship.
You never know, the person who made that decision realised it was a mistake too late, but was too embarassed to reverse it until you spoke up about it. This person can probably learn from this in the future. :)