Despite the ease of using the Console to push the Operations Manager agents out to your computers this is not really the most sustainable of processes. It works OK in your development environment and in small management groups but it is not really up to it in a larger production world.
It is far better to use a tool like Configuration Manager to install agents and keep them patched etc.
So, you know the command line installer settings for the Agent. It works when you run it from the command prompt, but the quiet installer fails when you add the /qn switch to the SCCM installer.
What is missing is the final switch, AcceptEndUserLicenceAgreement=1
Put this at the end of your installer command line and you are good to go with a quiet install of the SCOM agent.
See the rest of the switches here: http://technet.microsoft.com/en-us/library/hh230736.aspx