I've found a little info on this but figured I would run this up the flagpole to see if there are any gotchas that I may not be thinking of. We no longer require a gateway server and will be removing it. Thanks as always for any pointers

Reassign any agents pointing to the gateway to another server. Delete the gateway server out of the scom console Decommision the server. Pay special attention to the AD integration. When it runs through the Gateway server make sure you change the rule. It's doing common things uncommonly well that brings succes.