How can an employee take an ethical stand regarding a business decision when his or her superior already has taken a different position?

The employee can rationally discuss the decision and how they feel about it with the superior. Try to avoid conflict and try to use statements such as " I think" or " I believe" then back it up by facts. If you use those statements it leaves "wiggle room" so you’re not wrong. If you say that something is and it isn’t than they’re going to dismiss you as wrong.