The offended team is not making a choice of whether the rule got broken or not, but if they want the penalty to be applied. There are 2 examples of this is NCAA softball, catcher's obstruction and leaving the base early. However, this is not unique in the world of sports, in football for instance a team nearly always has the choice to decline a penalty. The logic behind this is to prevent a team from gaining an advantage by breaking a rule and having a penalty enforced that would be a more favorable result than the result of the play.