If you try to install the SCOM agent on a SharePoint server that already has the SCSM self-service portal installed, the install of the SCOM agent will fail. To resolve this the only option is to uninstall the SCSM self-service portal then install the SCOM agent and reinstall the SCSM Self-service Portal.
Since most of the configuration for the self-service portal is stored in the SCSM database this process can be done fairly easily as long as you have not done any major modifications to the self-service portal and where having a well-documented change process in place comes into play.
Update(7/9/2013): Also note that if the SCOM Management Server attempts to upgrade the agent after a update Rollup install this will result in the agent showing up under pending management under Failed Agent Installation.
This is very frustrating to me to find that I went through the work to reinstall the SCSM Self Service Portal so I could have sharepoint monitoring to have the agent broken later by an update.