You can't delete superagent repos, as they are defined by policy rather than created at the server end.
If a machine is a superagent and you don't want it to be, change the agent policy assigned to that machine. Once the machine has received the new policy and communicated the fact to the ePO server, you will no longer see that repo in the list.
Thanks vill have to run or create a new policy that gets rid of these in dirstributed system.
You should be able to just assign it the default agent policy instead of creating an entirely new policy.