The GM asks you to implement a certain directive that can harm the companies reputation? What is the best way to respond?

It depends on circumstances and your relationship but the key thing is to allow the GM an "out", which allows them to change their mind without feeling or looking foolish.

For example, introduce 'new information' that the GM could not possibly have known at the time they made the original decision.  Obviously you will need evidence to support your claim that the directive could harm reputation.

1. Reply GM the consequence only once. 2. Look for GMs reaction. 3. If GM accepts your view, proceed with proof submission. Else, do what GM wishes.

Its a challenging task, moreover GM or bossess prefer to consider ideas of those, they have already seen as result oriented.

However, do the analytical analysis of associated risks and consequences. Be diplomatic, design a presentation and add your ideas with result oriented examples and present to him at appropriate time.