You've just annotated your handicap with God. He does not conform to YOUR own definition of "morality". He is a diety to be worshipped on your own terms, not a Sovereign, Holy standard by which all truth and all morality may be measured and to whom all glory is given. It is your "own understanding" that is your god and not a higher power to whom you subject your will.
I think you should take this all in context. It is your position that God might ask and require some to carry out an act of unrighteousness. That is simply not the case. You do not know the motivations, justifications etc, therefore you call into question the validity of the order without full comprehension. You stand on shaky ground.
Furthermore, if God wanted to wipe out an entire race, He would not NEED our help to do it. Microbes (bacteria or viruses) do not have a conscience and would be sufficiently lethal to carry out any such task. Therefore, if you are asked by God to do anything, the question might be "why me?", but never "why that?". He chooses to give us the privilege of demonstrating our love and devotion to him in numerous ways. Sometimes they are controversial from a human perspective, sometimes difficult, but never have we been able to ascertain with our limited knowledge they are anything but righteous.